Former army commando M Moorthy's death last week touched off ethnic and religious tensions when Islamic authorities claimed the body, saying he had converted to Islam.
The Sharia religious court confirmed the conversion and the High Court said it could not overrule its verdict, meaning that Moorthy's widow Kaliammal Sinnasamy had no chance to argue her case.
Nazri Aziz, minister in the Prime Minister's Department, told the New Straits Times on Friday that when there was a dispute over conversions, the case should be heard in a civil court where all sides can be represented.
"When a person's faith is in question, the civil court should be allowed to hear it. Let evidence from both sides be produced," he told the daily.
"If we let the Muslim court decide this, justice might not be served because it would decide in favour of Islam."
Kaliammal has said she was stunned when the army informed her of Moorthy's "conversion", after he lapsed into a coma on 11 November at the age of 36.
Islamic authorities and army colleagues said Moorthy, who rose to fame after scaling Mount Everest in 1997 as part of a Malaysian mountaineering team, converted to Islam last year and changed his name to Mohammad Abdullah.
But Kaliammal denied the claim, saying he was not circumcised, ate pork and celebrated the Hindu festivals.
About 60% of the country's population are ethnic Malay Muslims, who live alongside substantial ethnic Indian and Chinese minorities.
Representatives of minority religions said on Thursday that racial harmony in Malaysia had been jeopardised by the Moorthy case, and that they feared Sharia courts were taking precedence over civil courts in Malaysia's dual-track system.