Yes, M.Sc integrated courses are available in NITs in all over India. NIT Warangal and NIT Trichy are the best institutes as per ratings and reviews offering integrated M.Sc in Physics.

• NIT Suratkal
• Motilal Nehru NIT Allahabad
• NIT Rourkela
• NIT Calicut
• Malviya NIT jaipur

NIT Rourkela also offers very good integrated M.sc in mathematics. This is one of the best courses here.
NIT Durgapur offers integrated M.Sc in Chemistry.
http://nitcouncil.org.in/index.php/site/console/siteVisitNIT