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Several shots were fired at around 03:00 local time (08:00 GMT) on Tuesday at the offices in San Antonio.
Two neighbouring buildings came under fire, but no injuries were reported, the FBI said in a statement.
The FBI said it was "reviewing surveillance footage" as part of its investigation into the shootings.
No arrests have been made and investigators are looking for suspects, according to US media reports.
In a statement, ICE blamed the shootings on "political rhetoric" and "misinformation" about the Trump administration's detention policies.
ICE under the Trump administration has been heavily criticised for its treatment of undocumented immigrants held at detention centres near the US-Mexico border.
"This disturbing public discourse shrouds our critical law enforcement function and unnecessarily puts our officers' safety at risk," said Daniel Bible, ICE's director for San Antonio.
The shootings were called "cowardly, brazen, violent acts" by Christopher Combs, head of the FBI's San Antonio operations.
US Immigration and Customs Enforcement officers carry out a raid in Sherman, Texas, in June
Mr Combs said those responsible for firing the shots "did some research" because they "knew what floors ICE was on, and they hit those".
"All of the shots that we have found are on the floors where ICE had offices," Mr Combs said, calling the incident "a very targeted attack".
Although no one was injured, Mr Combs said "we could be here today talking about the murder of a federal official" had the bullets "gone two inches in another direction".
Bullet holes can be seen in several windows at the buildings located near Brookhaven Drive, north-east San Antonio.
A picture tweeted by Ken Cuccinelli, acting head of Citizenship and Immigration Services, shows a bullet hole in a window at one of the offices targeted.
The building is mainly used for executive and administrative purposes, ICE said.
According to the Washington Examiner, the shooting is the latest of four recent attacks at ICE facilities across the country.
The three previous incidents happened in Washington DC, Tacoma, Washington and Aurora, Colorado, within days of each other in July, the website reported.
Given the current climate, FBI investigators fear there could be more attacks, Mr Combs said.
"We cannot allow political discourse to lead us to the point of violence, where federal employees, innocent people doing their jobs, are put in harm's way," he said.
