PALATKA, Fla. (AP) _ Amtrak pleaded innocent today to charges stemming from its practice of flushing passenger-car toilets and sewage holding tanks into Florida waterways as trains go over bridges.

Assistant State Attorney Paul Meredith said the federal railroad agency submitted its pleas to Circuit Judge Robert Perry by facsimile machine.

The plea was entered after Amtrak rejected a settlement offer from district state Attorney John Tanner, who promised to drop three charges of commercial dumping if Amtrak would stop all flushing while its trains cross trestles over creeks and rivers.

The company said it can't do that because it would set a precedent. Federal law permits the railway to dump its sewage on its right-of-way, and this overrides state and local regulations, Amtrak contends.

Amtrak has threatened to suspend service in Florida if Tanner presses his case but Tanner said Amtrak was bluffing.

Amtrak has come under fire in several Western states as well as Florida for the sewage dumping.

But the Putnam County case may be the first to go before a criminal judge. Amtrak spokesman Clifford Black has said the only other pending cases are two civil lawsuits in Oregon. There have been ''concerns and inquiries'' raised in other states, he said.

''They run the risk of losing passenger train service,'' said Black. ''That is something the various jurisdictions must consider.''

Agreeing to Tanner's plea bargain would make Amtrak a target for similar demands from anyone else wanting to stop dumping in any body of water in Florida, Black said.

''With the myriad waterways in Florida, it would be an impossible situation,'' he said.

Amtrak's 600 passenger cars dispose of sewage either by dumping directly onto the tracks when toilets are flushed or by spraying the contents of 30- gallon holding tanks when the trains are traveling at least 35 mph.

The company hopes eventually to replace much of its fleet with new cars that would have holding tanks for all toilets. Black said it would cost $147 million to install those tanks on the current fleet.