No one was hurt in the incident.
The girder slipped off the pillars and fell on a crane which was used to put it on two pillars during the intervening night, Minister for Works Naeem Akhtar told news agency PTI.
"The girder had just been installed on the pillars and had not been fixed yet.There is no structural damage to the flyover project due to the earthquake," Mr Akhtar said.
An official of the Economic Reconstruction Agency (ERA), the executing agency of the flyover project, said no one was hurt in the incident.
A 6.2 magnitude quake today jolted the Jammu and Kashmir and could even be felt in Delhi NCR. The epicenter of the warthquake was in Afghanistan.