But it was not immediately clear which employee was to be charged.
The investigation focuses on whether Cardinals front-office employees broke federal law by accessing the Astros database called Ground Control, which housed information on prospects. Investigators also have focused on whether senior officials at the Cardinals were aware of the spying.
The alleged breach began after Jeff Luhnow, the Astros general manager, left the Cardinals to take the Houston job. In the wake of the departure, some at the Cardinals appeared to believe Luhnow and others took proprietary information with them. The Astros database was similar to one the Cardinals used, but many teams have similar systems.
Luhnow has said the Astros created its own original database. Giles Kibbe, an attorney for the Astros, told the St. Louis Post Dispatch that neither the Houston team nor of any of its employees who came from the Cardinals stole any proprietary information from St. Louis.
In a statement to CNN later on Friday, Kibbe said the organization stands by "all of our previous comments," adding that the Astros look forward to the FBI concluding its investigation.
The Cardinals this week said they fired their director of scouting, Chris Correa, who is among the Cardinals personnel under investigation.
Cardinals General Manager John Mozeliak declined to say why Correa was let go.
"I can confirm he was on administrative leave and was terminated yesterday. I think, at this time, it's just best to understand it's an open investigation and any other comments are not in anybody's best interest," Mozeliak said.
The FBI did search a house used by Correa and other Cardinals staff during spring training.
Correa's attorney, Nicholas Williams, said: "Mr. Correa denies any illegal conduct. The relevant inquiry should be what information did former St. Louis Cardinals employees steal from the St. Louis Cardinals organization prior to joining the Houston Astros, and who in the Houston Astros organization authorized, consented to, or benefited from that roguish behavior."
The probe by investigators at the FBI's Houston office is complete, according to officials briefed on the matter, but is awaiting action by the Houston U.S. attorney's office. A U.S. attorney spokeswoman didn't respond to a request for comment.
A spokeswoman for the Houston U.S. attorney's office said "no charges have been filed and we obviously cannot provide any information that is not contained in our public court record nor confirm or deny the existence or non-existence of an investigation."
FBI spokeswoman Shauna Dunlap said the agency "aggressively investigates all potential threats to public and private sector systems."
"Once our investigations are complete, we pursue all appropriate avenues to hold accountable those who pose a threat in cyberspace," she said.
The intrusion isn't considered computer hacking. Instead, investigators believe Cardinals employees used an old password belonging to a former employee who went to work for the Astros in order to gain access to the Astros database.