Olympian Nathan Baggaley has been charged after a drug bust.

Australian Federal Police arrested the champion kayaker, 37, with another man, 52, on Friday night in Tweed Heads in northern NSW during an ongoing investigation into amphetamine trafficking.

The two-time Olympic silver medallist faces seven charges including manufacturing and producing a prohibited drug, supplying a large commercial quantity of a prohibited drug and conspiring to manufacture and import drugs into Australia.

The older man has been charged with one count of manufacturing and producing a prohibited drug.

Another man was arrested in Forster and charged with supplying a large commercial quantity of a prohibited drug and conspiracy to manufacture and produce a prohibited drug.

Baggaley won two silver medals at the Athens Olympics in 2003 and gold medals at the ICF Canoe Sprint World Championships in 2002, 2003 and 2005.

He has been remanded in custody and is expected to appear in Lismore Local Court on Monday.