"We extend an unqualified apology to the Hon Prime Minister of India and Hon Chief Minister of Tamil Nadu," said a statement posted on the Lankan Defence Ministry website.
It said the article titled 'How meaningful are Jayalalitha's love letters to Narendra Modi' had been published without appropriate authorisation and it has been removed from the website.
"The article which had been published without appropriate authorisation and not reflecting any official position of the Government of Sri Lanka or Ministry of Defence and Urban Development has since been removed," the statement added.
The article had appeared on the Lankan Defence Ministry's website along with a graphical portrayal of Prime Minister Modi and Chief Minister Jayalalithaa.
Hours after the article was published, it created a furore in India, with BJP allies PMK and MDMK seeking severing of diplomatic relations with the island nation.
Jayalalithtaa has urged Prime Minister Modi to seek unconditional apology from Lankan government over the article.