Anura Senanayake was remanded into custody until Wednesday pending further investigations into the May 2012 killing of national rugby skipper Wasim Thajudeen.
The Criminal Investigations Department told Colombo judge Nishantha Peiris it had evidence to suggest Senanayake, who retired last year, had conspired to suppress the investigation.
Sri Lanka arrests ex-president's son over money laundering
Police initially said Thajudeen had died in a road accident after his charred body was found inside his car in Colombo.
The body was exhumed in August last year, seven months after the new government came to power, and forensic experts ruled he had been tortured and killed.
Former president Mahinda Rajapakse, whose son Yoshitha is also a former rugby captain, has denied allegations by rival political parties and local media that he helped cover up the murder.
Thajudeen's body was exhumed after new evidence emerged that he had been abducted in a car owned by the Sri Lanka Red Cross Society, police told a court last year.
Sri Lanka police guilty of violating international law
The Red Cross said the Land Rover Defender belonged to the organisation, but it was being used at the time by a charity of the then-first lady, Shiranthi Rajapakse.
Both she and her husband also face investigation over allegations they syphoned off billions of dollars from the state during his decade in power.
Several Rajapakse siblings, as well as other family members and close associates face a plethora of corruption allegations, which they have rejected as a political witch-hunt.
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