The bodies of those who died were returned to Manila on Thursday. They were honoured on Friday in a ceremony led by President Benigno Aquino.
The violence took place in the southern province of Maguindanao on Sunday.
Police seeking two terror suspects entered a village held by the Moro Islamic Liberation Front (MILF).
MILF signed a peace deal with the government last year to end years of fighting.
But the rebels say police did not liaise with them about the operation as required under the deal, leading to the accidental clash.
On Friday, flags at government offices and military installations are being flown at half-mast to honour those who died.
At the memorial service inside a police camp in the suburbs of Manila, Mr Aquino paid tribute to the fallen officers by offering a prayer at each of their coffins.
He also presented each of their families with a Medal of Valor, the highest military award given by the armed forces.
"I pledge to bring justice to all those who were killed," said Mr Aquino, who faced criticism for not being present when the officers' bodies arrived in the capital
He promised grieving relatives that government forces would make it a top priority to capture suspected bomb expert Abdul Basit Usman.
Usman, who is linked to a MILF splinter group that rejects the peace deal, is one of two suspects that the commandos were targeting during the operation.
The other was Zulkifli bin Hir, known as Marwan, who is a leading figure of Islamist militant group Jemaah Islamiyah (JI)
Police say Marwan was killed, but this has not been confirmed. Both men have been incorrectly reported killed several times.
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On Wednesday, in a televised address to the nation, Mr Aquino said that the peace deal with MILF must not collapse.
"If the peace process were derailed, how many more graves would we have to dig," he said.
The rebels have agreed to end their fight in return for the establishment of an autonomous Muslim region.
Thousands of people have been killed over four decades of separatist fighting in the south of the country.

The approval of the austerity measure is an important victory for President Michel Temer.
He took office earlier this year promising to lead the country out of its worst recession in many decades.
Protests against the measure turned violent in the capital Brasilia and at least a dozen states in the country.
The opposition says the measures will mainly hit areas such as health and education, which are already underfunded.
Thousands of demonstrators took to the streets during the Senate session to protest against the austerity plan.
After the vote, many demonstrations descended into violence.
In Brasilia, masked protesters set fire to a bus and marched on the local offices of Globo TV, which they say is biased towards Mr Temer's government. But the marchers were blocked by riot police.
In Sao Paulo, the headquarters of the state's conservative Industrial Federation (Fiesp) was attacked.
To pass the constitutional amendment, the government needed the votes of 49 senators - three-fifths of the Senate.
The measure was approved by a narrower margin than the government expected, passing by 53 to 19 votes.
"We have won. That was the main thing: to deliver the product in the middle of a storm," said government leader in the Senate Romero Juca.
The project, known in Brazil as PEC 55, freezes expenditure in the executive, judiciary and legislative branches of power, allowing them to grow only by the rate of inflation n the previous year.
The government argues it is necessary to boost growth and investments, and contain the country's growing public deficit.
But critics say the poorest in society will be harmed and that setting a spending cap for two decades in advance is unrealistic, says the BBC's Julia Carneiro in Rio de Janeiro.
The measure takes effect on Thursday.
The Philippines is holding a day of mourning for 44 police commandos killed in a clash with Muslim rebels.
[NEXT_CONCEPT]
The Brazilian Senate has approved a controversial amendment to the constitution capping public spending for the next 20 years.