Turkish police have captured the suspected jihadist who slaughtered 39 people on New Year's night at an Istanbul nightclub, detaining him in a raid on a residential area of the city after a long manhunt.

The alleged assailant was found along with his four-year-old son in an apartment in the Esenyurt district of Istanbul after a massive police operation, state-run TRT television reported.

The attacker had been on the run for over two weeks, after slipping into the night following the attack on the glamorous Reina nightclub on the Bosphorus.

Reports had previously suggested he never left the Turkish metropolis, despite a tightening of borders in a bid to stop him escaping, triggering fears that a dangerous killer was on the loose in the city.

The Islamic State (IS) group took responsibility for the bloodbath, the first time it has ever openly claimed a major attack in Turkey.

It had previously been blamed for several strikes including triple suicide bombings at Istanbul airport in June.

The suspect was caught in an operation jointly carried out by the Turkish police and the spy agency MIT, Turkish TV said.

Turkish media published a picture of the detained man with blood on his face and T-shirt, his neck gripped by a policeman.

Television images showed him being roughly led away, his head bent low.

There had been confusion over the identity of the attacker in the wake of the massacre, with reports initially suggesting a Kyrgyz national and then a Uighur from China.

But reports on January 8 said intelligence services and anti-terror police in Istanbul had identified him as a 34-year-old Uzbek who was part of a Central Asian IS cell.

The state run Anadolu news agency identified the detained man as Abdulgadir Masharipov, while the Dogan news agency said he used the code name of Ebu Muhammed Horasani within IS.

These are the same names given in the January 8 reports.

The suspect was living in an apartment rented by a Kyrgyz in Istanbul who was also detained, TRT reported. Anadolu said a total of five people were detained in the operation, including three women.

Anadolu added the suspected attacker had been brought to the Istanbul police headquarters for questioning. It said other raids took place on IS targets in the city, without giving further details.

NTV television said the attacker was captured at a quarter past midnight (local time). The police had spotted his location three days earlier, but preferred to track him to identify his contacts.

The son is under protection, the reports said.

Turkish media reports had said that the gunman was a well-trained killer who had fought for IS in Syria and had gained weapons expertise there.