© Provided by The Independent Archaeologists for HS2 will dig up and rebury thousands of bodies from a church graveyard to make way for the railway.
Critics say it shows a lack of respect, but HS2 says all human remains removed will be treated with "dignity and care", and that the work will shine a light on almost 900 years of history at the site.
The remains of the medieval St Mary's Church in Stoke Mandeville, Buckinghamshire, will be excavated so that work on the high-speed London-Manchester line can continue.
The church was built in 1080, shortly after the Norman conquest, and was renovated in the 13th, 14th and 17th centuries.
The burial ground was in use for 900 years, with the last recorded interment in 1908. The building was abandoned and eventually demolished, leaving a pile of rubble that became overgrown with vegetation and less visible to the public.
All human remains found - expected to number about 3,000 - will be reburied in a local spot still to be identified, according to HS2, with a specially created monument.
Excavations began in February, and before the exhumations started, the Bishop of Buckingham gave them a virtual blessing.
HS2 says the site is unique and the scheme is providing "a rare opportunity to excavate and understand the history of this building and how its use and meaning changed over time".
Helen Wass, of HS2, said: "All artefacts and human remains uncovered will be treated with dignity, care and respect, and our discoveries will be shared with the community through open days and expert lectures.
"HS2's archaeology programme seeks to engage with all communities, both local and nationally, to share the information and knowledge gained as well as leaving a lasting archival and skills legacy."
Politics lecturer Adrian Hilton tweeted: "And here's me thinking the best way to honour the dead is to respect their places of interment and leave them in their graves, ashes to ashes, dust to dust."
But Clare Kirk, a genealogy writer, said her great grandmother's ancestors were buried there, adding: "As an archaeology enthusiast, I'm looking forward to their findings and I know that the remains will be treated with the utmost respect."
Building the £106bn north-south rail link, the world's most expensive railway ever created, involves destroying 108 ancient woodlands, 693 wildlife habitats and 33 legally protected sites of special scientific interest, to the anger of nature lovers.
© Provided by The IndependentBuckinghamshire residents call for HS2 to be halted to protect wildlifeGetty Images
Opponents say they have seen bird boxes, bat roosts and irreplaceable trees being torn down, at a time when society should be enabling biodiversity to recover.
The Wildlife Trust says the plans "come at an unacceptable cost for our natural world, putting the homes of wildlife, including barn owls and otters, at risk", and the RSPB said the scheme had "descended into an example of worst, rather than best, practice".
Activists trying to protect habitats have repeatedly clashed with HS2 security guards.