Police carried out simultaneous operations in several cities and raided the homes of five allegedly senior Al-Qaeda operatives, the Hurriyet newspaper reported, giving an updated arrest toll of 23.
It said those arrested were accused of sending fighters to Syria, raising money for Syrian rebels under the guise of seeking charitable donations, and providing arms for Al-Qaeda.
The Humanitarian Relief Foundation (IHH) said its offices in the southern city of Kilis were also searched and computers seized in what it branded a "smear campaign" linked to the corruption scandal embroiling the government.
It said one of its staff was arrested but denied any Al-Qaeda links.
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The IHH claimed it was a victim of the feud between Erdogan and a powerful exiled Islamic preacher at the root of the worst political crisis since Erdogan took office in 2003.
"This smear campaign is backed by people inside and outside Turkey," IHH secretary general Yasar Kutluay told AFP, in an apparent reference to the movement headed by influential cleric Fethullah Gulen who lives in the US but wields considerable clout in the judiciary and police in Turkey.
The head of the anti-terrorism unit leading the Kilis raid was subsequently removed from his post, local media reported.
Erdogan's government has since December sacked hundreds of police and prosecutors involved in the graft probe, accusing them of being part of a "state within a state" trying to topple his administration.
Today's raids come almost two weeks after Turkish media reported that security forces had stopped a truck loaded with weapons on the Syrian border and arrested three people including a Syrian.