Turkey on Wednesday denied claims that it was blocking NATO vessels deployed in the Aegean Sea from launching a mission to help stop the flow of migrants from Turkish shores to EU territory.

"Turkey has been the mastermind" of the proposed mission -- details of which have been held up by discord between Turkey and Greece -- foreign ministry spokesman Tanju Bilgic told a weekly press briefing in Ankara.

"To claim that Turkey opposes its own proposal is neither logical nor consistent," he added, branding the allegations as "absurd, unrealistic and fabricated."

A Western diplomatic source told AFP on Tuesday that, despite requests by the NATO operation's German command, "the Turks refused" this weekend to allow the vessels to enter Turkish waters.

The unprecedented mission, which seeks to tackle migrant smugglers, was launched last month and aims to help the European Union cope with its worst migration crisis since World War II.

A spokesperson for the German defence ministry also said: "Reports that Turkey blocks the deployment of German ships in its territorial waters are not correct."

But the spokesperson confirmed that talks with the Turkish side on the operational area were continuing.

"The planning is well on track and will be finalised probably in the coming days."

The NATO mission to monitor smugglers was first announced by Turkish Prime Minister Ahmet Davutoglu and German Chancellor Angela Merkel on February 8 in Ankara.

Under the plan, NATO forces will conduct reconnaissance, monitoring and surveillance to provide information to Greece, Turkey and the EU's border agency Frontex so that they -- not the alliance -- can deal with the traffickers.

Greece and Turkey are at loggerheads over Aegean airspace and territorial waters, which have held up agreement on the operational details.

Asked whether there was a risk that the NATO mission could trigger a Turkish-Greek dispute in the Aegean, Bilgic said those issues would be discussed at a bilateral level.

"Our goal is that NATO carries out its activities there without triggering problems between the two countries. We are exerting efforts in that regard," he said.