Fars said the fishermen, all Iraqi nationals, were seized in recent days together with six boats.
"Despite repeated warnings, some Iraqi fishermen enter Iranian territorial waters illegally and over-fish the waters," senior coast guard official Yadollah Sharafi said.
"After the completion of the necessary investigation, three (crew members) were returned to their country and the nine others remain in custody," he said.
Neighbouring Iran and Iraq fought an eight-year war in the 1980s, but ties improved after the US-led invasion of Iraq that toppled Sunni strongman Saddam Hussein in 2003.
However, bilateral relations were strained when a small contingent of Iranian troops moved into an oilfield inside Iraqi territory in December, raising the Iranian flag over an inactive oil well.
The dispute, which Tehran called a "misunderstanding," ended in January when troops withdrew after talks between the two countries' foreign ministers.
