Critics have accused Arroyo, who is due to step down in 2010, of trying to use the proposed change to extend her term in office.
The plan includes a power-sharing structure between the president and the newly-created prime minister for three years, after which the latter would become head of a British-style parliament.
Jose de Venecia, the speaker of the house of representatives, said the debate was shelved following the public outcry.
"We are not insensitive to public opinion," he said late on Monday, a day after Filipinos responded to calls for nationwide prayers and protests by powerful Catholic bishops.
"We are not insensitive to public opinion"
Jose de Venecia, speaker of the house of representatives
One bishop even called on soldiers to join them but the invitation was quickly shot down by military leaders intent on stamping out plotting by disgruntled troops.
General Hermogenes Esperon, the military chief, said: "Instead of calling us to undertake protest actions it will be better for these people to pray."
To cool things down, de Venecia said the lower house would now call for elections next year, coinciding with congressional and local polls.
A mass rally organised by the influential Catholic Bishops Conference of the Philippines scheduled for December 17 in Manila is expected to attract hundreds of thousands.
The government on Tuesday brushed off fears of unrest from the rallies.
Norberto Gonzales, the national security adviser, said: "We have fears some radical groups might take advantage of the situation, but we're confident that they don't have the capability to topple the government."
Followers have been asked to avoid bringing political banners and placards.
Monsignor Pedro Quitorio, a spokesman for the conference, said: "What they [the lowers house] did Monday night did not solve our problem. What we still need is prayer."