The controversy began after the website published an article which portrayed Indian prime minister Narendra Modi and Tamil Nadu chief minister Jayalalithaa in a derogatory manner.
"An article titled 'How meaningful are Jayalalitha's love letters to Narendra Modi?' had appeared on our website along with a graphical portrayal of Hon. Prime Minister of India and Hon Chief Minister of Tamil Nadu," read a statement hosted on the defence ministry's website.
It said that the article "which had been published without appropriate authorization and not reflecting any official position" of the Sri Lankan government or the defence ministry has since been removed.
"We extend an unqualified apology to the Hon Prime Minister of India and Hon Chief Minister of Tamil Nadu," it added.
The article had a picture showing Jaya dreaming about Modi.
Bharatiya Janata Party allies MDMK and the PMK had sought strong action against the island nation.
PMK chief S Ramadoss said that the article was 'bad' in taste. It demeaned Jayalalithaa and Modi, he said. He also alleged that the visit of a BJP delegation led by party leader Subramanian Swamy, who is considered to be close to the Sri Lankan administration, had emboldened that country to make such remarks, said a IBN Live article. "The Sri Lankan President (Mahinda Rajapakse) and Defence Secretary should apologise for the article. If the Sri Lankan government declines to do so, India should not hesitate to sever its relations with that country," Ramadoss said.
MDMK leader Vaiko described the incident as 'unforgivable' . It showed the 'atrocious' nature of the Lankan army, he said.
Jayalalithaa's letters to Modi were not mere communication, but her 'struggle' to ensure the welfare of the Sri Lankan Tamils, he said.