Those affected are of Turkish descent and had been publicly critical of Recep Tayyip Erdogan, the Netherlands public broadcaster NOS reported.
Dual nationals from Germany, Switzerland and other European nations were having trouble returning home, the broadcaster said.
Many had been in the country on holiday or to visit relatives, with some accused of supporting the “Hizmet” movement led by US-based cleric Fethullah Gulen.
A spokesperson for the Dutch foreign ministry said it was difficult to confirm how many citizens were affected as it only knew of those who had sought help.
“The reasons why [they have had problems leaving Turkey] are varied, but some of them may be linked to the Gulen movement,” she told The Independent.
“We are prepared to help people who actively seek assistance.
“We immediately raised the inconvenience caused to these people with the Turkish authorities.
“Inquiries show that other countries’ citizens are having similar problems in Turkey.”
Mr Erdogan accuses the Gulen movement of plotting a failed coup in July and classes members as “terrorists”, resulting in purges seeing 42,000 people including teachers and journalists detained or dismissed for alleged support.
European nations and the US have cast doubt on the claims, with a recent report by the House of Commons Foreign Affairs Committee finding that evidence of the Gulen movement’s involvement was “anecdotal and circumstantial”, as was evidence used for its terrorist designation by the Turkish government.
The dispute is one of several issues worsening tensions between Turkey and its EU allies, amid a continuing row over cancelled rallies by Turkish government ministers.
They had been dispatched to drum up support among expats for a “yes” vote that would give Mr Erdogan dramatically increased powers in a constitutional referendum to be held later this month.
But authorities in the Netherlands, Germany, Austria and other countries cancelled planned rallies on safety grounds, sparking accusations of “Nazi practices” from Ankara.
The row worsened last month as thousands of Turks protested when the Netherlands prevented foreign minister Mevlut Cavusoglu from flying to Rotterdam and banned ministers from speaking.
A statement from the Prime Minister, Binali Yildirim, threatened that Turkey would retaliate in the “harshest ways” and “respond in kind to this unacceptable behaviour”.
Mr Erdogan has threatened to renege on a deal struck with the EU aiming to prevent refugee boat crossings to Greece, while hitting out at human rights concerns levelled at his government.
The Turkish embassy in London referred The Independent to its embassy and consulate in the Netherlands, which did not immediately respond to a request for comment.