Two of the city's subway lines - the A and the C - have been crippled and may not return to normal capacity for three to five years after a fire Sunday afternoon in a Lower Manhattan transit control room that was started by a homeless person trying to keep warm, officials said yesterday.

The blaze, at the Chambers Street station used by the A and C lines, was described as doing the worst damage to subway infrastructure since the terrorist attack of Sept. 11, 2001. It gutted a locked room that is no larger than a kitchen but that contains some 600 relays, switches and circuits that transmit vital information about train locations.

The A line will run roughly one-third the normal number of trains - meaning that riders who used to wait six minutes for a train might now have to wait 18 minutes - while the C train will cease to exist as a separate line, at least for the time being. The C will be replaced by the V in Brooklyn. Long waits and erratic service are likely to be the norm on the two lines, which have a combined ridership of 580,000 each weekday.

Riders on the West Side of Manhattan and in the Brooklyn neighborhoods of East New York and Ocean Hill-Brownsville will find the available trains more crowded, and will likely seek alternate subway lines, crowding them as well.

"This is a very significant problem, and it's going to go on for quite a while," said Lawrence G. Reuter, the president of New York City Transit. He estimated it would take "several millions of dollars and several years" to reassemble and test the intricate network of custom-built switch relays that were destroyed in the blaze, which officials believe began when the homeless person - who has not been found - set fire to wood and refuse in a shopping cart in the tunnel about 50 feet north of the Chambers Street station.