Mr Stamper, who had been due to step down soon after six years in the job, said he would stay until March to help investigators. He hoped his departure would "depoliticise" the inquiry into police behaviour during the 135-nation conference.
WTO delegates, many of whom were trapped in hotels last Tuesday by chanting protesters, were stung by tear gas as they tried to continue the talks. They say police and the Seattle authorities in effect sabotaged the event by failing to keep demonstrators at a safe distance.
Civil-liberties groups and residents' associations have accused the police of violating the constitution when they set up a "no protest" zone around the WTO meeting and arrested hundreds of peaceful protesters. They accuse the police of excessive force by using tear gas, pepper spray, water cannon and rubber bullets.
Seattle mayor Paul Schell, who also faces investigation, praised Mr Stamper as a man "of absolute integrity". But that praise was not enough.