The cost of the most expensive Rail Baltic route through Harju County is 100 million euros more expensive than the cheapest route through the county.
The project's leaders have so far failed to choose a route through the nation's most heavily populated county, with the track mostly already agreed upon for the rest of Estonia.
There are five directions with 12 alternative tracks for the county. Indrek Sirp, head of Rail Baltic's Estonian operation, said that none of them can be ruled out at this stage.
He said the Cabinet will debate the problem today, but they are waiting for further studies.
The most expensive track (12A) would be one built on existing Tallinn-Pärnu lines, as it goes through the city and other residential areas.
The longest route would be through the planned Nabala nature reserve on the border with Rapla County, but environmental minister Keit Pentus-Rosimannus said she is against that option, as she said the environmental damage would be too great.
Rail Baltic, when completed, will connect Estonia, Latvia and Lithuania to the high-speed transport system widely used in Europe.