Police searched the premises of the Humanitarian Relief Foundation (IHH) in southern town of Kilis near the Syrian border, the charity's vice president Huseyin Oruc told AFP on Tuesday.
"We see this as part of a dirty plot," Oruc said, adding that the police had not given a reason for the action.
On January 1, Turkish media reported that security forces had stopped a truck loaded with arms and ammunition on the Syrian border and arrested three people including a Syrian.
The drivers claimed they were carrying aid on behalf of IHH but the organization denied the allegations as "slanderous".
Interior Minister Efkan Ala also denied the reports, saying the truck was shipping aid to the Turkmen community in the country.
IHH press coordinator Serkan Nergis told AFP that Tuesday's early morning operation was launched by local counter-terrorism units.
"Police forced our staff out and wanted to confiscate our documents and computers," he said, adding that the standoff was still going on.
The Turkish government has repeatedly denied it is involved in sending weapons to rebels fighting the Syrian government.
However, in December, local media -- quoting UN and government documents -- reported that Turkey had shipped 47 tons of arms to the militants since June last year.
Media reports also said Friday that police had seized two buses near the Syrian border that were carrying weapons and ammunition secreted in the baggage hold.
NTJ/BA