Turkish counter-terrorism police have raided the offices of an aid agency on the border with Syria, in what local media described as an operation in six cities against individuals suspected of having links to al-Qaeda.

The Humanitarian Relief Foundation (IHH) said police on Tuesday raided its offices in the southern Turkish city of Kilis, which borders Syria, and detained one person.

"We see this as part of a dirty plot," said the charity's vice president, Huseyin Oruc, noting police had not given a reason for the raid. The IHH denied any ties to al-Qaeda.

"IHH aid is delivered to Syrian babies, children and those who freeze in the cold... This is an operation to change perceptions [about IHH] and stop aid from being delivered inside Syria," the group added in a statement.

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 organisation denied the allegations as "slanderous". Interior Minister Efkan Ala also denied the reports, saying the truck was shipping aid to the Turkmen community.

Suspects detained

The IHH, which is considered close to the Turkish government, organised the flotilla of ships carrying aid to Gaza that was raided by Israeli commandos in 2010.

IHH press coordinator Serkan Nergis said 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.

The Dogan news agency said police launched counter-terrorism raids in Istanbul and five other cities, detaining at least two senior al-Qaeda suspects.

Turkey has maintained an open-door policy throughout the Syrian conflict, providing a lifeline to rebel-held areas by allowing humanitarian aid in and giving refugees a route out.

But the rise of al-Qaeda-linked groups such as Jabhat al-Nusra and the Islamic State of Iraq and the Levant (ISIL) in parts of northern Syria near the border has left Ankara open to accusations it is lending support to radical Islamists, a charge Prime Minister Recep Tayyip Erdogan has repeatedly denied.