(Reuters) - A group of protesters set fire to the wooden door of Mexican President Enrique Pena Nieto's ceremonial palace in Mexico City's historic city center late on Saturday, denouncing the apparent massacre of 43 trainee teachers.

The group, carrying torches, broke away from what had been a mostly peaceful protest demanding justice for the students, who were abducted six weeks ago and apparently murdered and incinerated by corrupt police in league with drug gang members. 

Police put out the flames and enforced fencing designed to keep the protesters away from the National Palace, which was built for Hernan Cortes after the Spanish conquest and now houses Mexico's finance ministry.

Pena Nieto lives in a presidential residence across town, and was not in the palace at the time.

Tens of thousands of people in recent weeks have taken to the streets of Mexico City and those of the southwestern state of Guerrero where the students were abducted to decry the government's handling of the case in recent weeks.

The case is the toughest challenge yet to face Pena Nieto, who took office two years ago vowing to restore order in Mexico, where about 100,000 people have died in violence linked to organized crime since 2007. 

At least two people were injured in Saturday night's protest, local television reported. Riot police cleared the square before midnight and an ambulance was assisting the injured people.

(Reporting by Elinor Comlay; Editing by Simon Gardner)