He said he was quitting "to avoid embarrassment to the government". He denies wrongdoing.
Opposition has been protesting over Mr Raja’s alleged role in the sale of second generation (2G) licences.
Federal auditors reportedly estimate that billions of dollars were lost as a result.
Mr Raja – who belongs to the DMK party, an ally of the governing Congress party – has been accused of issuing licences on a "first-come first-served" basis instead of auctioning them, reports say.
In May, India’s auction of third generation (3G) bandwidth for mobile phone services ended with the government reaping $15bn, twice the sum expected.
There are about half a billion mobile phone subscribers in India, the world’s fastest growing mobile market.
Last week, two senior members of India’s governing Congress party resigned over separate corruption allegations.
Ashok Chavan quit as the chief minister of western Maharashtra state amid allegations he was involved in homes meant for war widows being transferred to politicians and military officers.
Controversial Commonwealth Games organiser Suresh Kalmadi also quit his party post.