Police searched two houses and arrested five people during the operation to detain the suspect behind the Istanbul nightclub attack, ITV News understands.
It is believed three women and two men have been detained.
According to police sources, the man entered Turkey from Iran, but since the attack in the early hours of New Year's Day has never left Istanbul.
The suspect was pictured wearing a bloodied grey t-shirt and was taken to a city hospital under a large police escort on Monday evening.
Some police sources suggest he has changed location up to four times.
The suspected gunman behind the Istanbul nightclub attack was found at a house belonging to a Kyrgyz friend in a special police operation in Istanbul's Esenyurt district, according to private NTV television.
Hurriyet newspaper and other media identified the suspect as Abdulkadir Masharipov, an Uzbek national.
ITV News understands he is currently being treated in hospital for unknown injuries.
Media reports said he would 'undergo medical checks' before being taken to a police headquarters for questioning.
Dogan news agency published an image showing a bruised, black-haired man in a grey, bloodied shirt being held by his neck. NTV television said he had resisted arrest.
The suspected gunman had been on the run since the attack.
The suspected gunman who killed 39 people in an Istanbul nightclub on New Year's Day has been caught in the city's Esenyurt district, according to various Turkish media.
Islamic State claimed responsibility for the attack, which it said was revenge for Turkish military involvement in Syria.
Soon after the attack, Turkish authorities identified the main suspect who they said was a member of the Uighur community - a Muslim group who lived in western China.
Authorities in Turkey have established the possible links and location of the main suspect behind the New Year's Day attack at an Istanbul nightclub.
In an interview with broadcaster A Haber, the country's Deputy Prime Minster Veysi Kaynak said he could not rule out the possibility of the gunman fleeing abroad.
It is believed the suspect is a member of the Uighur community - a Muslim group who live in western China.
He also said it was clear the attacker acted alone, but could have been helped by others.
- Video report by ITV News Security Editor Rohit Kachroo
As CCTV footage emerged showing the Reina nightclub gunman just hours before the attack, Turkish police announced they had detained 58 people in connection with the attack across three cities in Turkey.
A third of those detained are children.
ITV News has also learnt that the suspected gunman used a fake passport and an alias to rent several homes in the weeks before the attack, yet despite the information they already hold, Turkish authorities have so far failed to find the attacker.
Police in Istanbul have arrested 20 people as they continue to hunt for the gunman behind the attack on Reina nightclub which left 39 people dead and up to 70 wounded.
Authorities increased security around the city on Wednesday as they arrested 20 people with suspected links to the deadly attack, Turkish media reported.
Police in Turkey have released a photograph showing the alleged Reina nightclub attacker arriving at a bus terminal to purchase a ticket to Istanbul.
Turkish authorities claim he walked into the ticket hall in Konya with his friend several days before attack.
Although they claim to have identified the suspect, they have not released his identity publicly.
Video footage has emerged allegedly showing the Istanbul nightclub attacker leaving the Zeytinburnu district for the Reina nightclub.
The CCTV video, obtained by ITV News, was recorded at 10.49pm on December 31 and shows a man walking down the road wearing a hooded coat and carrying a large rucksack.
It is believed the rucksack contained the weapon that he used to kill 39 people during a mass shooting at the nightclub less than two hours later.
A Turkish official has said changing the country's anti-terror laws would pose a threat to its national security.
The European Union wants Turkey to amend its anti-terror laws in order for its citizens to gain visa-free travel to Europe.
The initiative is part of a wider deal, signed last year, that is hoped would stem the flow of refugees and illegal migrants into Europe from Turkey.
However Turkey's EU minister, Omer Celik, reiterated Ankara's position that Brussels should not expect them to change their stance.
Turkish President Tayyip Erdogan has said "nobody's lifestyle is under systematic threat" following the New Year's Day attack on an Istanbul nightclub.
Mr Erdogan gave his comments during a speech to local administrators at the presidential palace in Ankara, and said the shooting was a deliberate attempt the divide the nation.
In an address that was broadcast live on Wednesday, he said: "There is no point trying to blame the Ortakoy attack on differences in lifestyles.
"Nobody's lifestyle is under systematic threat in Turkey. We will never allow this."