The government moved resolution was passed with 144 votes in favour, 10 against and 37 abstentions in the 225-membered house.
"That this Parliament resolves that the investigation to be conducted against Sri Lanka by the Office of the United Nations High Commissioner for Human Rights should not be carried out on the ground that such a course of action is detrimental to the process of reconciliation and peace and that it erodes the sovereignty, dignity and stature of Sri Lanka", the resolution said.
The government received a jolt ahead of the vote when a key ally, Sri Lanka Muslim Congress, said they were boycotting the parliament debate on the resolution.
Party leader, Rauff Hakeem, who is also the Minister of Justice said they were skipping parliament as the government had failed to provide security to the Muslims against a communal riot in the southwestern region.
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"We are convinced that the government did not do anything to prevent the violence", Hakeem said.
At least 4 Muslims were killed while nearly 100 were injured in the attacks blamed on the Buddhist majority BBS or the Forces of Buddhist Power.
Sri Lanka's lack of action to control inter-religious tensions was highlighted by the UN rights chief Navy Pillay during her visit to the island last year.
Stepping up the international pressure, the European Union today urged the Sri Lankan government to uphold the rule of law.
"We condemn the outbreak of violence which resulted in the loss of lives and extensive damage to property," a EU statement said.
In a resolution backed by the US moved at the UNHRC meeting in Geneva in March, the council endorsed UNHRC chief Navi Pillay's recommendation for an external probe into the alleged war crimes in Sri Lanka. Unlike in 2009, 2012 and 2013, India had voted against Sri Lanka but in 2014 it abstained from voting on the resolution.