When asked whether India was backing armed Baloch militants, Musharraf told TV channel CNN-IBN in an interview aired on Sunday: "There are lot of indications, yes indeed."
There is a "lot of financial support, support in kind being given to those who are anti-government, anti-me and to those feudal people who are anti-national," he said.
A spat erupted this month after India expressed concerns about the situation in Balochistan.
India on Saturday rejected earlier Pakistani charges of involvement in Balochistan.
"As far as any allegations about India's interference in Balochistan are concerned, I would like to categorically reject these allegations as being utterly baseless and false," Indian foreign ministry spokesman Navtej Sarna said.
Musharraf said he hoped the dispute over Balochistan would not hurt the peace process between the two neighbours. "It should not be a setback to the process of dialogue of resolution (of disputes).
Musharraf said he was "annoyed" and "disappointed" by New Delhi's statements and alleged actions in Balochistan.
"It's a direct interference in our internal affairs," he told CNN-IBN.