PHF secretary Asif Bajwa told a news conference on Wednesday the Indian federations had pulled out of the tournament scheduled from April 9-13 on the advice of its foreign ministry.
"We are obviously disappointed with this development because Malaysia had also first confirmed they would take part in the event and then pulled out two days back," he said.
Security reasons have also prompted Bangladesh soccer league champions Sheikh Jamal Dhanmondi to withdraw from an Asian football tournament.
Jamal were due to play Erchim FC (Mongolia), KRL Football Club (Pakistan) and Taiwan Power Company (Chinese Taipei) in group A of the AFC President Cup at the Punjab Stadium in Lahore from May 8-12.
'We have informed the Bangladesh Football Federation through a letter that we will not go to Pakistan as it is not a very safe country," Sheikh Jamal president Manzoor Kader told reporters.
The Pakistan Cricket Board is trying to convince the Bangladesh board to send the national team for a three-match one-day international series this month.