The charge of violating the U.S. Clean Water Act by discharging oil into the bay is one of four criminal counts pending against Cota in connection with a Nov. 7 oil spill from a container ship.
Cota, 60, of Petaluma, was piloting the Cosco Busan when it struck a protective fender at the base of the Bay Bridge and sustained punctures to two fuel tanks, through which nearly 54,000 gallons of heavy bunker fuel spilled into the bay.
He is scheduled to go on trial on Oct. 20 in the court of U.S. District Judge Susan Illston on the pollution charge as well as a count of killing migratory birds and two counts of making false statements on medical forms.
Last month, Cota's lawyers asked Illston to dismiss the charge of violating the Clean Water Act on the ground that he had no criminal intent.
But prosecutors in a response filed late on Thursday argued that Cota's request was "wholly without merit."
The prosecutors wrote that Congress specifically intended to make the alleged action a crime when it amended the Clean Water Act in 1990 to include criminal penalties for negligent as well as deliberate discharge of oil.
The amendment was a direct response to the massive Exxon Valdez oil spill in Alaska in 1989, the federal lawyers said.
They wrote, "Punishing marine operators with jail time for negligently causing large oil spills was precisely what Congress had in mind" when it passed the amendment.
Illston will hold a hearing on July 18 on Cota's request for dismissal of the pollution charge, as well as on a separate request for dismissal of the two false statements charges.
Cota is accused of negligence in failing to review the ship's course and navigational equipment adequately; sailing in heavy fog and then failing to proceed at a safe speed; and failing to use the ship's radar during the final approach to the Bay Bridge.
In a separate action, Cota's lawyers told a state pilot commission last week that he will retire as a state-licensed pilot as of Oct. 1.