MPs from Mr. Rajapaksa's Sri Lanka Podujana Peramuna (SLPP)-led coalition said they would now represent themselves independently.
The decision comes as the South Asian country struggles with power outages and shortages as a result of economic and currency crises.
This has sparked widespread rallies calling for Mr. Rajapaksa's resignation.
At this time, it is unknown what the consequences of the MPs' conduct will be. They've distanced themselves from the government but haven't thrown their weight behind the opposition.
However, it may cast doubt on the prime minister's authority over parliament.
The president and his brother, Prime Minister Mahinda Rajapaksa, have so far refused to resign.
Instead, he urged opposition parties to assist him in forming a national government and accepting cabinet positions.
They've all refused, and they've all demanded that he resign.
"What the people want is for this president and the entire administration to resign," said Sajith Premadasa, the leader of Sri Lanka's major opposition alliance, the Samagi Jana Balawegaya.
Angry Sri Lankans demand that the president resign.
A newly appointed finance minister announced his resignation on Tuesday, less than 24 hours after assuming the position.
Ali Sabry, a close confidant of President Rajapaksa, said he would give up his parliamentary position for someone "fit to handle the crisis" from outside politics.
Meanwhile, anti-government rallies in key cities around the country resumed on Tuesday.
Demonstrations asking for the president's resignation have gained traction in recent days.
After a demonstration outside the president's house got violent on Thursday night, protesters disobeyed a curfew that was supposed to stretch from Friday to Sunday in order to disrupt a planned day of protests.
Mr. Rajapaksa, who swept into office with a majority vote in 2019, vowing stability and a "strong hand" to lead the country, has seen his popularity plummet as a result of the protests. Due to a currency shortage, Sri Lanka is now unable to pay for petrol and other imports, exacerbating the country's greatest economic crisis since its 1948 independence from the United Kingdom.
The country requires foreign cash to pay for fuel imports.
"Essentials such as fuel and cooking gas are in constant limited supply. Hospitals are in the danger of closing due to a lack of drugs "Maithripala Sirisena, Sri Lanka's former president and leader of the Sri Lanka Freedom Party, told parliament that his party had withdrawn its support for Mr. Rajapaksa's alliance.
"At this time, our party is on the people's side."
As discontent increases over rising food and fuel prices, Sri Lanka's cabinet and central bank governor have all resigned. President Gotabaya Rajapaksa has extended an invitation to all political parties to join a new administration. Those who have turned to the streets in protest, however, vow they will not stop until Mr. Rajapaksa resigns as the country's economic crisis worsens.
The screams and placards are largely directed at one guy across an island brimming with rage and desperation.
They say, "Go Gota Go," "Go Gota Go."
Gota refers to Gotabaya Rajapaksa, the country's divisive president, whom many blame for the country's catastrophic position.
"He needs to go; he's taken everything from us," said Nadhie Wandurgala, who joined her husband and two daughters in defying a country-wide curfew to protest on Sunday.
She told how her family had gone from living in comfort to everyday discomfort, with power outages lasting up to 17 hours, a daily race to find gas to cook with, and huge lines to buy gasoline for their automobile.
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