The four organisations include two feminist groups and a media production house, according to the METRO centre for press freedoms which organised a news conference in Sulaimaniyah to criticise the decision.
PKK fighters have several positions in Iraq's northern autonomous Kurdistan region, which also hosts Turkish military bases used to strike Kurdish insurgents.
Ankara and Washington both deem the PKK, which has waged a decades-long insurgency in Turkey, a terrorist organisation.
Authorities in Sulaimaniyah, the Iraqi Kurdistan region's second city, have been accused of leniency towards PKK activities.
But the Iraqi federal authorities in Baghdad have recently sharpened their tone against the Turkish Kurdish insurgents.
Colonel Salam Abdel Khaleq, the spokesman for the Kurdish Asayesh security forces in Sulaimaniyah, told AFP that the bans came "after a decision from the Iraqi judiciary and as a result of the expiration of the licenses" of these groups.
The move to ban the groups has nonetheless sparked anger, with METRO centre director Diyar Mohamed denouncing it as being "the fruit of external pressures".
"This decision is political and not judicial, we strongly condemn it," he told AFP.
He described the decision as "unjustifiable", adding that none of the groups had been involved in any "partisan activity", according to a statement by METRO.
In March, following a visit to Iraq by top Turkish officials, federal authorities in Baghdad quietly classed the PKK as a "banned organisation".
By mid-August, Baghdad and Ankara had signed a military cooperation deal to establish joint command and training centres with the aim of fighting the PKK.
Tawar Adel, the head of the Gezengi Barbayan production house, said security forces had arrived at their headquarters on Tuesday to order them to stop working.
"We were surprised by the ban on our company. Since 2017, we have had the official licence of the Kurdish ministry of commerce and we renewed it in May 2024," she said.
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