When MI6 set up home on the banks of the Thames one secret escaped its watchful eyes. The oldest wooden structure ever found on the river, timbers almost 7,000 years old, have been discovered buried in the silt below the windows of the security services' ziggurat headquarters at Vauxhall, south London.

The archaeologists who uncovered the six hefty timber piles had to explain to the security services what they were up to when armed police turned up after they were spotted pottering about on a foggy day in the mud, armed only with tripods, cameras and measuring equipment – not, as one spectator had apparently reported, shoulder-mounted rocket launchers.

"They accepted there wasn't much damage we could do with a tripod," said Gustave Milne, the archaeologist who leads the Thames Discovery programme that has been surveying the entire prehistoric foreshore, uncovering centuries of ancient wharves, fish traps, jetties and ship timbers.

The timbers, partly scoured bare by erosion of the river bed, the largest up to a third of a metre in diameter, were discovered in work during exceptionally low tides last February, but carbon dating work – revealed in the new edition of London Archaeologist journal – has only recently been completed, proving that the trees were felled between 4790 BC and 4490 BC.

Although the site is now exposed only at the lowest tides, the ancient Thames was narrower and deeper, and Milne believes that 7,000 years ago the timbers may have been built on dry land, possibly at the highest point of a small island.

"The find is very interesting, because in the mesolithic period the people were nomadic hunter-gatherers, living in temporary camps – not at all given to building substantial structures like this," Milne said.

"At the moment we don't have enough timbers to give any kind of alignment, they're not in a straight or a circle – but they could have supported a substantial platform with some form of domestic structure or dwelling."

The site is just where a smaller river, the Effra, enters the Thames, and it was clearly important to the prehistoric Londoners. The archaeologists, working with experts from the Museum of London and English Heritage, also found worked flint from the same date as the timbers, older pottery, and just upstream, on the far side of the modern Vauxhall bridge, a much later Bronze Age structure.

"There may have been a ford, it may have had some religious significance, or it may just have been very rich hunting grounds – but it was clearly what my colleague at the Museum of London calls 'a memorable place'," Milne said.

"We're just sorting out which are the lowest new year spring tides to go back for another look – if Mr Bond will let us."