"The government has strongly condemned the development," Sushma Swaraj said in the Rajya Sabha.
"We will certainly summon the high commissioner of Sri Lanka and convey this to him," the minister said.
This came after the upper house saw disruptions over the issue, losing its question hour.
The upper house saw two adjournments during the question hour as AIADMK members trooped near the chairman's podium raising the issue.
An objectionable article about Jayalalithaa and Modi was published on the Sri Lanka's defence ministry web site last week, and was taken down in a hurry.
Sri Lanka also offered an "unqualified apology" for the article.