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(CNN) —  

When President Donald Trump slammed the brakes on delivering military aid to Ukraine in June, he tapped then-national security adviser John Bolton and Defense Secretary Mark Esper to conduct a policy review.

A senior administration official said the directive to freeze Ukrainian aid came in June, earlier than has previously been reported – a move that continues to baffle US officials. Four months later it is still unclear exactly why the President ordered the review or what was under review.

The Pentagon had already announced the plan to provide the millions of dollars in military aid to Ukraine. Bolton had opposed the freeze on Ukrainian aid from the outset. And the previous month the Department of Defense and the State Department had notified congressional oversight committees that aid to Ukraine was ready for distribution.

The grab bag of explanations the administration has offered for the hold up – and the President’s continued fixation on the Biden family – has fueled suspicion that the delay was politically motivated.

The recently revealed whistleblower complaint describes other events happening at the time of the freeze, namely the phone call between Trump and Ukrainian President Volodymyr Zelensky in which Trump asks for a “favor.”

The President tweeted Monday that the explanation was “Very Simple!” He has insisted he wasn’t withholding aid from Ukraine as political leverage to convince Ukrainian officials to investigate his political rival, former Vice President Joe Biden, and Biden’s son, Hunter.

“I was looking for Corruption and also why Germany, France and others in the European Union don’t do more for Ukraine. Why is it always the USA that does so much and puts up so much money for Ukraine and other countries?” Trump tweeted. “By the way, the Bidens were corrupt!”

There is no evidence of wrongdoing by Joe or Hunter Biden.

The unusual process the Trump administration went through to freeze foreign aid sparked confusion at the Pentagon, on Capitol Hill and among agency staffers, including at the Office of Management and Budget, according to congressional aides, administration officials and the whistleblower complaint.

Department of Defense officials were particularly perplexed by Trump’s June request for another review of the military aid to Ukraine, according to defense officials.

Assessments like these are typically conducted before departments make their notifications to Congress, according to congressional aides and former budget officials. And in this case, the Defense Department had already assessed the aid package and John C. Rood, the under secretary of defense for policy, had made that clear to congressional committees in a May letter.

“On behalf of the Secretary of Defense, and in coordination with the Secretary of State, I have certified that the Government of Ukraine has taken substantial actions to make defense institutional reforms for the purposes of decreasing corruption, increasing accountability and sustaining improvements of combat capability enabled by U.S. assistance,” Rood wrote.

When Trump demanded another assessment, the Pentagon moved quickly and recommended that the freeze be lifted. The extent of what Defense Department did as part of the renewed policy review has not been explained. There’s no indication that Esper believed the review could have been a politically motivated stalling tactic. Still, the funds remained frozen. Officials at the Defense Department started referring questions to the White House and the Office of Management and Budget.

Sources told CNN at the time that they were waiting for Bolton to return from a trip to Kiev, even though Bolton had been opposed to the freeze.

Meanwhile, confusion was spreading.

In interagency meetings on July 23 and July 26, OMB officials “again stated explicitly that the instruction to suspend this assistance had come directly from the President, but they were still unaware of a policy rationale,” according to the whistleblower complaint.

An administration official confirmed that interagency meetings took place on both dates — further confirmation that much of the whistleblower’s complaint was accurate. But the administration official downplayed the revelations in the whistleblower complaint, saying it was mainly lower-level officials in attendance and it wouldn’t be surprising if they didn’t know the policy rationale behind the delay.

Lawmakers were also trying to figure out what was going on. Acting White House chief of staff and OMB Director Mick Mulvaney was pushing for a funding reduction plan that would have cut about $4 billion in foreign aid and lawmakers initially believed Ukraine aid was been caught up in that battle.

Then congressional aides started to get the unofficial word from their Pentagon contacts: The money was being held up. They also started to hear from defense contractors who reached out to say contracts were being suddenly suspended and it was unclear why, according to congressional aides.

Congressional aides said they weren’t formally notified about the freeze.

A senior administration official said they had no obligation to inform lawmakers of the delay. “Congress does not like to be out of the loop when it comes to anything spending-related, but this was not in their jurisdiction,” the official said. “It’s the President’s decision.”

As officials across the US government struggled to understand the delay, Trump spoke by phone on July 25 with Zelensky. After Zelensky mentioned military assistance, Trump turned the conversation to his requests that Ukrainian officials investigate the Biden family.

The White House insisted there was nothing inappropriate about the call and said the President had legitimate reasons for holding up aide to Ukraine.

“The President has done nothing wrong and to suggest otherwise is an attempt to deliberately mislead – which is exactly what Adam Schiff shamelessly tried to do,” said White House spokesman Hogan Gidley, in a jab at the House Intelligence Committee Democratic chairman who is leading the impeachment inquiry. “While we don’t discuss internal deliberations, the President has been clear he wants other countries to eradicate corruption, and that he wants our international partners to start doing their fair share.”

The Trump administration finally unfroze aid to Ukraine on September 11, after lawmakers threatened to force an amendment vote that would have put Republicans in a tough spot of picking whether to stand with Trump or on the side of Ukraine military funding.

By then, Trump had soured on Bolton – the man he entrusted with his Ukrainian policy review – and fired him the day before releasing the funds. Bolton declined to comment.

Esper, meanwhile, said the delay didn’t cause any harm.

“At this point, most of the money is out the door. And at no time or at any time has any delay in this money, this funding, affected US national security,” Esper said last week. “We will provide to Congress and whomever, whatever information we can provide with regard to this incident.”

On Wednesday, the Trump administration notified Congress it was prepared to formally announce an arms sale to Ukraine involving Javelin anti-tank missiles – the weapons Zelensky expressed desire to purchase on his call with Trump in July.

CNN’s Barbara Starr, Ryan Browne, Lauren Fox, Kevin Liptak and Zachary Cohen contributed to this report.