Members of the leftist Party of the Workers presented the condoms to mark International Women's Day as they picketed the headquarters of the influential Catholic Bishops Conference.
They also asked the bishops to bless the two baskets but no bishop was present at the time to respond.
"We humbly ask the bishops to bless the condoms as a conciliatory gesture to unite for reproductive health and women?s rights," said Judy Ann Miranda, the party's secretary-general.
The bishops have since also called for a ban on Condom advertising but the government has shrugged off their demands.
In reaction to the protest by the Party of the Workers, the bishops' spokesman Monsignor Pedro Quitorio said they could not compromise on the church's opposition to birth control devices.
"If contraceptives are immoral, nothing can change that.
About 75 million Filipinos, out of a national population of 93 million, are Catholics, a legacy of the country's Spanish colonial past.
The Roman Catholic Church disallows the use of artificial contraceptives like condoms, even for preventing the spread of disease.