Police said on Monday they had agreed with Muslim community leaders to distribute the cards in Muslim areas in Manila, which has suffered a series of bombings attributed to Islamic fighters.
"An identity card just for Muslims would be unfair," Imam Alem Ali Baulo of Manila's Golden Mosque said on Tuesday.
"If the government wants an ID system, it should be for all Filipinos, Muslim and Christian alike," he said.
Filipinos are not required to carry identity cards, although the issue has been hotly debated for years.
Islamic fighters set off a series of bombs in Manila in December 2000. The southern Philippines is home to four armed groups seeking a separate Islamic state and is suspected of being a training ground for the al-Qaida-linked Jemaah Islamiah.
About 800,000 of Manila's 12 million people are Muslim. Most of them live in poor and crowded neighbourhoods that are a magnet for criminals and Muslim fighters escaping conflict in the south.
Police said the proposed ID card system was modelled on an ID card system already in place at the Golden Mosque, which issues cards to residents and visitors in an effort to screen potential troublemakers. The mosque is Manila's largest.
But Jose Asayo, police chief in the Muslim neighbourhood of Quiapo, denied the plan was discriminatory.
"If the government wants an ID system, it should be for all Filipinos, Muslim and Christian alike"
Imam Alam Ali Baulo,
Golden Mosque, Manila
"Those who do not want the IDs are those who have something to hide. If you have a clean record, you won't object," he said.
The Philippines government has not publicly commented on the police proposal.
Aga Acmad, who sells pirated DVDs in a small shop in Quiapo, said he disagreed with the plan. "If they want to impose IDs, that is fine, but let it be for everyone," he said.
On Monday, senator Aquilino Pimentel likened the plan to the system used in Nazi Germany in which Jews had to wear the Star of David badge.
Earlier this month, Philippine police seized explosives and firearms bound for a Muslim neighbourhood of Manila.
The Philippines, a former US colony, is one of Asia's staunchest backers of U.S. President George Bush. A 96-member Philippine team is currently in Iraq.