Turkish President Recep Tayyip Erdogan on Tuesday expressed fury at the surprise resignation of his influential spy chief and said his arch enemy, the US-based preacher Fethullah Gulen, had wreaked more havoc on the country than Kurdish militants.

The head of Turkey's National Intelligence Organisation (MIT) Hakan Fidan resigned at the weekend to stand for parliament, with Erdogan then stunning commentators by saying he did not approve of the move.

Fidan has always been seen as one of Erdogan's most loyal allies and his motives in wanting to stand for parliament and enter politics remain unclear, with some believing he is eying a top government job.

"I told him (Fidan) loud and clear: 'I don't believe that your leaving is right'," Erdogan was quoted by the Hurriyet daily and DHA news agency as telling reporters on his plane while travelling to Colombia.

"I don't find it appropriate," said Erdogan, adding that Fidan had explained that he was "exhausted" and could no longer go on in the position.

"Unfortunately, he thinks that taking such a step is appropriate for himself and so took it," said Erdogan, reaffirming he had appointed Fidan to the post to be his "secret keeper".

Observers have been at a loss to explain the situation, given that Erdogan is usually seen as all-powerful number one and Prime Minister Ahmet Davutoglu his obedient servant.

Commentator Murat Yetkin, analysing Erdogan's latest comments, described the situation as an "emerging and unexpected internal row".

"It could be... a challenge he is facing from his closest circle, from the two men he has been relying on so far," he wrote in Hurriyet Daily News, referring to Fidan and Davutoglu.

Erdogan said Fidan's resignation was particularly unfortunate at a time when the authorities are fighting the so-called "parallel state" purportedly run by Gulen.

Erdogan has launched an all out war against his former ally Gulen, an Islamic preacher based in the United States who has extensive interests in Turkey in finance, banking and media.

He said that not even the Kurdish separatist Kurdistan Workers' Party (PKK) -- which has waged a deadly three decade insurgency for self-rule -- had caused as much damage.

"Today not even the terrorist PKK has caused as much damage for Turkey as the parallel structure," he said, accusing Gulen of making contact with foreign governments to besmirch Turkey's reputation.