Two men arrested on Friday following counter-terror raids in Sydney have no links with terrorism and will apply for bail on Monday, their lawyer says.

Omar Ammouche, 33, and Jibryl Almaouie, 21, were charged after separate raids in Sydney's south-west.

Ammouche was arrested at a Greenacre home on Friday and charged with acquiring and possessing ammunition subject to a prohibition order and without having a permit.

Almaouie was charged with weapons offences after a raid in December at a home in Condell Park, where police allegedly found guns and ammunition.

Neither man appeared when their cases were dealt with at Parramatta Local Court.

Lawyer Adam Houda, who represented both men, was questioned about the arrests by reporters outside court.

"These matters are absolutely nothing to do with terrorism or terror-related issues," Mr Houda said.

He said the prosecution's case against his clients was weak and they would apply for bail on Monday at Bankstown Local Court.

Both men will remain in custody over the weekend.

The raids were part of a long-running investigation into domestic terrorism threats and support given to Australians fighting overseas.

Investigators seized documents and computers, which are being forensically examined.