Turkish Defence Minister Nurettin Canikli said officials "discovered a nearly three-thousand strong structure" in the armed forces, state news agency Anadolu reported.

"In the coming days they will be dismissed by emergency decree. We have sent (the paperwork) to the prime ministry," Canikli said in parliament.

Turkey introduced a state of emergency five days after the July 15, 2016 attempted overthrow of President Recep Tayyip Erdogan.

The state of emergency was renewed for the seventh time on Wednesday after parliament approved a three-month extension.

The emergency has come under heavy scrutiny as the government has used decrees to suspend or sack over 140,000 public sector employees including teachers and soldiers over alleged links to US-based Muslim preacher Fethullah Gulen or Kurdish militants.

So far, 8,568 Turkish armed forces personnel have been sacked in a major purge of the military. This includes 150 generals, over half its pre-coup contingent of top ranking officers.

Turkey claims Gulen ordered the coup but he denies the accusations.

The European Commission on Tuesday urged Turkey to "lift the state of emergency without delay" in its latest report on Ankara's bid to join the EU.

"The broad scale and collective nature, and the disproportionality of measures... such as widespread dismissals, arrests, and detentions, continue to raise serious concerns," the Commission wrote.

But Canikli defended the state of emergency saying it had "only affected terror organisations, terrorists and their supporters", Anadolu quoted him as saying.

"No one has been impacted. And it will continue to have no effect on anyone else."