Two more Melbourne suburbs have dodged getting Skyrail as part of the state government's level crossing removal program.

Rail tracks on the Frankston line at Edithvale and Bonbeach will be sunk, Public Transport Minister Jacinta Allan announced on Sunday.

But a third crossing at Seaford will be built onto an embankment because a trench cannot be dug without affecting groundwater, a creek and wetlands.

There had been speculation the Frankston line could get elevated rail like the Caulfield to Dandenong section of the Cranbourne-Pakenham line as part of the government's blitz to increase safety and reduce traffic jams.

Last week the government announced the Cheltenham and Mentone stations on the Frankston line would also be sunk.