"If anyone is hurt by my statement, I express regret over it," he said in a video statement.
The minister's statement came after a meeting between BJP national general secretary Ram Madhav and PDP leaders in Jammu on a range of issues, including Ganga's controversial statement, which had led to public bickering between the alliance partners of PDP and BJP.
Ganga had reportedly called stone pelters as traitors.
"There is only one remedy for them and that is bullets. And if not bullets, they should be given punishments like the youths who are beaten with sticks by forces. Take my word that next time they (the youth) won't throw stones," he was quoted as saying by the local media.
"My entire focus was targeted at the National Conference which had made a statement on the issue (of stone pelting)," he added.