"We have previously expressed our concerns about the legal process in Saudi Arabia and have frequently raised these concerns at high levels of the Saudi Government. We reaffirm our calls on the Government of Saudi Arabia to respect and protect human rights, and to ensure fair and transparent judicial proceedings in all cases," the State Department said in a statement.
"We are particularly concerned that the execution of prominent Shia cleric and political activist Nimr al-Nimr risks exacerbating sectarian tensions at a time when they urgently need to be reduced," the statement continued. "In this context, we reiterate the need for leaders throughout the region to redouble efforts aimed at de-escalating regional tensions.
Meanwhile, White House Deputy National Security Adviser Ben Rhodes told reporters that "there needs to be greater relations between the communities in the Middle East."
He added that the U.S. "broadly have concerns about human rights in Saudi Arabia."
Human rights group Amnesty International had called the charges against Nimr vague
and pronounced his death sentence "appalling." The group said the case against him was part of a systematic effort by the majority Sunni government to crush dissent among the nation's Shiite Muslim minority.
The other executed individuals were convicted for acts of terror and having extremist ideology, including some who were a part of plotting and carrying out the 2004 attacks against civilians on the U.S. Consulate in Jeddah.
Saudi Arabia remains one of the United States' most crucial allies in the Middle East, a longstanding relationship built on oil money and national security interests.
"Sometimes we have to balance our need to speak to them about human rights issues with immediate concerns that we have in terms of countering terrorism or dealing with regional stability," Obama said in an interview with CNN's Fareed Zakaria.
The President did say, however, that his administration continues to apply "steady, consistent pressure" on the Middle East nation on issues such as human rights, a position reiterated by Rhodes on Saturday.
"We have urged the Saudis to show restraint with respect to human rights," he said.