Charities, community groups and individuals were encouraged to plant trees in the run up to the celebrations this summer.
The Woodland Trust alone planted three million saplings, while organisations funded by the Government's Big Tree Plant have planted almost 300,000 during the tree-planting season from November to March.
Around ten per cent of the trees were ash, which are often imported from Europe.
Mary Creagh, Shadow Minister for the Environment, said the trees could have been infected with ash dieback that has killed off woods in Europe and now threatens the UK's forests.
“A lot of trees were planted this season. What a shame if some of them spread the disease or end up being burned or going on to die of this disease eventually.”
Although the ash trees would not spread the disease this summer, because of the lifecycle of the fungus, dieback that is not spotted threatens woodland.
Ms Creagh pointed out that ash dieback was first spotted on an imported plant in a nursery in the UK in February this year and the Government was warned about the risk of the disease coming into the country as early as 2009.
But the Government only banned imports and took action to monitor outbreaks this autumn.
She said that if members of the public had known then more rigorous checks could have been carried out to ensure ash planted for the Jubilee were not infected and perhaps to even plant different species.
"Why did ministers keep the public in the dark?" she asked
Ash dieback is now on 155 sites around the country, according to the latest figures from the Forestry Commission. The young trees on 15 nurseries and in 55 recent plantings will be felled and destroyed. Already more than 100,000 specimens have been burned. More mature trees on a further 85 sites in the wider environment are being monitored closely.
David Heath, the Environment Minister, insisted that the outbreaks in the wild were “consistent” with the disease blowing over from the Continent, where it is widespread, suggesting there was nothing the Government could have done.
He mocked Ms Creagh for her “conspiracy theory” that scientists were exaggerating the possibility of spread by the wind to cover up the Government’s complacency over banning imports.
"I'm sure you are right. We have an international conspiracy of all the leading forestry scientists in the world who have decided that they want to manufacture evidence in order to fit some theory concocted in the bowels of my department,” he said.
"Really, grow up. Look at the map, look at the facts, look at the evidence."
The Woodland Trust said they could not be sure if any of the ash trees planted for the summer were imported, since nurseries do not label if saplings have been “grown on” abroad.
The charity said all the sites planted this summer have been cleared for ash dieback and in future only trees sourced and grown in the UK will be planted. Just seven trees, that were traced back to an infected nursery were destroyed.
The Trust pointed out that ash dieback can only spread on leaf litter the summer after the tree has been planted.
Scientists believe the tiny mushrooms on the leaves, that release the spores, only grow after the fungus has had a chance to breed in the leaf litter.
"Ash trees planted for the Queens Jubilee would have been planted last winter and given any onward spread of Chalara is by spores produced on fallen leaves the summer after they fall those tree planted for the Queens Jubilee cannot of caused any onward infection to other trees over this summer as has been suggested," said a spokesman for the Woodland Trust.
Prof Michael Shaw agreed that the trees will not have spread spores this summer.
But he said the disease may not yet be showing in many of the imported trees so there is still a risk that dieback could spread from the imported trees in the future.
"Keeping it out would have been better because it is hard to detect whether we have successfully eradicated it."
Prof Shaw said scientists can use genetics to find out whether the ash dieback found in Britain in the widl was spread on the wind or from imports.
However, the different strains of the disease may be so mixed up it will be impossible to tell.
Zac Goldsmith, the Tory MP for Richmond, urged all people to “buy British”.
“It is absurd we are importing ash trees,” he said.