The Indian Foreign Ministry has conveyed "strong displeasure" to Chang Jae-bok, the top Korean diplomat in Delhi, who was summoned over the "unacceptable social media post by Hyundai Pakistan".
The post was shared on Twitter by a Pakistan unit of the car manufacturer on 6 February, extending solidarity with people in disputed Kashmir, favouring their separatist move.
On Tuesday, South Korea's Foreign Minister Chung Eui-Yong held a phone call with his Indian counterpart Subrahmanyam Jaishankar, conveying deep regret over "the offence caused to the people" and the Indian government by the social media post.
"India welcomes investments by foreign companies in various sectors. But it is also expected that such companies or their affiliates will refrain from false and misleading comments on matters of sovereignty and territorial integrity", a strongly worded statement issued by the Indian government read.
Soon after the 6 February post, Indians expressed their anger against the firm by making #BoycottHyundai a top trend on Twitter.
"Let us remember the sacrifices of our Kashmiri brothers and stand in support as they continue to struggle for freedom", Hyundai Pakistan wrote on Twitter and Facebook on Saturday with the hashtag #KashmirSolidarityDay.
Hyundai has apologised for the remark and distanced itself from any comments on political and religious issues in any specific region.
India and Pakistan have fought three wars over Kashmir since gaining independence from Britain in 1947. Although both Delhi and Islamabad claim Kashmir in full, they each control only parts of it - territories recognised internationally as Indian-administered Kashmir and Pakistan-administered Kashmir.