A media report, citing a Sri Lankan "ministerial source", claimed that the Lankan president accused the United National Party (UNP) - senior coalition partner - of not taking the alleged conspiracy to kill him seriously.
The minister, who declined to be named, claimed that the president said that India's external intelligence agency RAW was behind the plot.
Sri Lankan government also rejected the media reports as "baseless and false".
"The Ministry wishes to emphasize that relations between Sri Lanka and India including at the highest levels of government are strong, encompassing multiple spheres including intelligence sharing". This was reported in the local media widely.
"The rest of the houses will be given to firms which are ready to build them at lower prices", Senaratne told reporters in Colombo, the Sri Lankan capital, adding that China could also be considered in future for the remaining housing projects. It is stressed that those news are completely untrue.
According to media reports, Sirisena claimed that the Indian national could have been a "rogue" RAW agent, of which the Indian PM was not aware.
Modi appreciated the prompt steps taken by Sirisena and his government to "firmly refute the malicious reports", the statement said.
The Sri Lankan finance and media minister Mangala Samaraweera had previously strongly denied that there was any plot to kill Sirisena.
"We were just shocked when he said it", a source said, requesting anonymity. "What can now be done is to look at the genesis of this story and how it came about".
Kumara had also worked as an informant of the police. "In the meeting, the President emphasized the need to conduct a comprehensive investigation into the alleged assassination plot", it said.
The cabinet meeting witnessed heated exchanges when the ministers discussed the awarding of the East Terminal of the Colombo port to India, reports said.
Critics have said a big Chinese port project and related infrastructure in Sri Lanka's south have been dragging the country of 21 million people deep into debt.
The Cabinet spokesperson, however, on Wednesday said Sirisena had not expressed opposition to the Eastern Port Terminal deal with India.
Sirisena said he regards Modi as a "true friend of Sri Lanka" and a "close personal friend".
Sirisena took to Twitter to announce that he had a "successful telephone conversation" with Modi, who "assured India's fullest cooperation towards the development and prosperity of Sri Lanka".
Security for Sri Lankan President Maithripala Sirisena has been stepped up following the discovery of an alleged plot to assassinate him, two of his advisers said on Thursday. A Deputy Inspector-General suspected to be involved in the plot was suspended by the police based on Kumara's testimony.