The police officer says he was thrown to the ground by the firefighter after he told the officer to get out of the way as emergency teams arrived.
The incident has created tension between the two departments.
Chicago Mayor Rahm Emanuel wants to combine the city's police and fire marine units. But that might be harder than expected given what is alleged to have happened on the first night of November.
At just after 1 a.m., November 1, emergency crews were dispatched to the Chicago River near Goose Island, where two men were reported to have fallen in the water. First, the fire marine unit arrived, then their police counterparts.
Police officer Joseph J. Smith of the marine unit says he was assaulted by Captain Mark Altman, a firefighter who is the son of former Chicago fire commissioner Edward Altman.
Smith says Altman became enraged when the police boat showed up and told Smith to "get back" from the water's edge as firefighters worked. When Smith ignored him, Altman allegedly threw Smith to the ground. Smith filed a battery case, and in a statement said, Altman's "actions were totally out of line... any ordinary citizen would have been arrested on the spot."
People at Altman's home on the Northwest Side would not answer the door when ABC7 called looking for his side of the story. Earlier reports quote him as saying the incident was "overblown."
The Chicago Fire Department will only say its internal affairs division is investigating.
For the man in charge of the City Council's public security at the political level, this turf war is excusable.
"I know the firemen and the policemen, and they work together," said Alderman James Balcer.
When asked if there is worry that clout may be used in the investigation, Balcer said, "It is under investigation, so let's find out first before any accusations are made."
Mayor Emanuel, who wants to save money by combining the two departments' marine units, did not comment on the matter, nor on a fire department e-mail from Commissioner Robert Hoff's deputy that instructed CFD personnel to not cooperate with the city's inspector-general on information requests unless cleared through Hoff.
The police union would not comment on camera, but said via telephone that they expect the fire department "to do the right thing" in its internal investigation.
Chicago police at this point have not said what they are prepared to do, only that the matter is under investigation.
Firefighter Altman remains on the job pending his department's investigation.