Archaeologists fear 1,000 years of history may be shovelled into skips as time runs out on a key site in London. Harvey Sheldon, an officer of the London and Middlesex Archaeological Society, called the situation at the church of St George the Martyr, in Southwark, where substantial evidence of Roman buildings may be destroyed without being recorded, "a disgrace".

Yesterday he made a last ditch appeal to church authorities to give more time for excavation, before heavy machinery moves onto the site.

Southwark, once seen by archaeologists as a nondescript marshy suburb on the wrong side of the river from the Roman city of London, has through recent excavations emerged as a key part of the Roman administration of Britain. Other sites a stone's throw away have produced startling Roman finds, including a tomb claimed to be that of a woman gladiator, the oldest inscription with the placename "Londinium", and a monumental bronze foot, all that remains of a huge public statue. Dr Sheldon believes the evidence from a contemporary major Roman building is now about to be destroyed without record at St George's.

The archaeologists from the Museum of London Archaeology Service, who are working against the clock under contract for the church authorities, within the crypt, are now clearing out of the site. The construction work is part of a lottery-backed project to lower the crypt floor to make it suitable for community work.

Machinery is due next week for pile-driving and underpinning work, which will destroy anything in the archaeological layer that has not already been salvaged or recorded.

Dr Sheldon - who has himself directed many excavations in Southwark, including the Rose Tudor theatre site - believes the losses will include brick foundations, which may be from a major Roman building fronting onto Watling Street, one of the most important Roman roads whose precise route through the area has never been traced.

The present Georgian church, with its stepped tower, is something of a landmark in the heart of London's Borough district. The church has many associations with Charles Dickens, whose father and family were imprisoned for debt in the Marshalsea nearby, and who set parts of Little Dorrit in the church.

Dr Sheldon believes at least a month's further archaeological investigation is needed, which he estimates would cost £50,000.

"I have seen them myself, substantial brick foundations, clearly Roman from the quantities of Roman pottery coming out of the trenches. Levelling the site means that a metre of history is going to be scoured off the site and lost forever."

The Reverend Maggie Durran, the development consultant for St George's, said: "We are very keen on our archaeology, and we have done the very best we can by this site, but we have an absolute deadline of this week. Archaeologists have to understand that if their budget is spreading, everyone else's is shrinking."

Dr Sheldon says the problem lies in the way the brief for the excavation was drawn: he has no criticism of the team's actual work. Under government guidelines developers, in this case the church, must pay for rescue archaeology when building work involves destroying historical evidence. Work at St George's apparently slowed down when the archaeologists uncovered hundreds more buried human remains than expected. English Heritage gave an emergency grant for extra diggers over the weekend to recover medieval terracotta fragments judged of national importance which were also uncovered in the excavation.