The groups issued a joint statement demanding the release of Ruwan Weerakoon, a reporter with the Nation newspaper, who was arrested this week.
"We request the Inspector General of Police to disclose the reasons behind the arrest and detention of Ruwan Weerakoon and make arrangements for him to receive legal aid immediately," the statement added.
Weerakoon maintained close contact with Fonseka when the general led the military during the final phase of last year's war against Tamil Tiger rebels.
Fonseka was an ally of President Mahinda Rajapakse when the rebel Liberation Tigers of Tamil Eelam (LTTE) were crushed in May, but the two men later fell out and contested the presidency in January's elections.
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Fonseka was arrested soon after losing the poll and appeared in front of a court martial this week. The case was adjourned.
Local and international rights groups have accused Rajapakse of cracking down on dissent, a charge the government has denied.