Mr Tóibín said the desecration of the landscape around Tara was shameful, short-sighted and beyond belief.
The motorway, which passes through Co Meath, could cut journeys between Co Cavan and Dublin by an hour at peak times.
The 60km tolled scheme – with a €1 billion price tag – provoked legal action and angry protests over its route past the historic Hill of Tara and archaeological complex.
Mr Tóibín spoke out from Co Kerry, where he was chairman of the Listowel Writer’s Week.
“In a time when Ireland needs places which have a sacred aura and a special beauty more than ever, it is sad to see those who have misruled our country ganging up on our heritage.”
The author joined a long list of Irish artists – including Seamus Heaney, Paul Muldoon, Louis le Brocquy, Jim Fitzpatrick, Robert Ballagh and the Chieftains – who have previously criticised the location of the motorway.
Campaigners and environmentalists battled unsuccessfully since 2003 to force the Government to re-route the motorway away from the land around Tara.
The controversy over the roadway will continue for years as Tara was nominated to Unesco to be a World Heritage Site and listed as one of 100 Most Endangered Sites by the World Monuments Fund.
Elsewhere they maintained the European Commission is taking a case against Ireland for breaching the Environmental Impact Assessment Directive.
Vincent Salafia, of TaraWatch, said activists have been completely vindicated in their campaign against the route of this road. “The majority of Irish people, including most of our leading artists, as well as the EU and the major international archaeological bodies, have condemned it.
“The same reckless disregard for ethics, rights and regulation that brought down the economy, was employed to bulldoze this road through.
“The real kicker is yet to come, when traffic levels will show that the taxpayer will start paying millions of euros every year to the toll company, because traffic fails to meet the traffic guarantee which was secretly written into the M3 contract by the NRA (National Roads Authority).”
However, Transport Minister Noel Dempsey, who officially unveiled the motorway, which bypasses Dunshaughlin, Navan and Kells, said it was one of the biggest road projects to open in Europe this year.
Around 1,800 people were employed in its construction, with about 80 staff set to work at the its offices and toll plazas.