Baldia factory fire wanted frontman Abdul Rehman alias Bhola reached Karachi on Tuesday, DawnNews reported.
Rehman arrived at Karachi's Jinnah International Airport from Bangkok under custody of two Federal Investigation Agency (FIA) officials.
FIA's Counter-Terrorism Wing's Deputy Director Badar Bin Baloch and Inspector Rehmatullah supervised Rehman's immigration clearance at the airport.
The accused was then taken to an undisclosed location for further investigation.
Bangkok Police arrested Rehman on Dec 3, Thai police had reported.
Rehman, 46, is an accused in the 2012 arson attack at Karachi's Baldia garment factory in which 250 workers were burnt alive.
He was detained at a hotel in the red light district Nana area of the capital on Friday evening, Thailand's Interpol chief had said.
Rehman was arrested by the FIA with the help of Interpol, Additional IG Mushtaq Mahar had said.
“As per existing law, the FIA is authorised to arrest an absconder from another country with the help of Interpol,” said the AIG.
The fire at the Ali Enterprises factory in September 2012 was one of Pakistan's worst industrial disasters.
A judicial probe into the blaze was damning, pointing to a lack of emergency exits, poor safety training for workers, the packing in of machinery and the failure of government inspectors to spot any of these faults.
Initially the fire was believed to be an accident but a Joint Investigation Team ‘reinvestigating’ the case this year termed the incident a “planned sabotage and terrorist activity”.