The revelation, unearthed by a Sunday Herald investigation, has prompted First Minister Alex Salmond to accuse Hammond of deceiving parliament. Salmond has also written to David Cameron demanding an apology.
The problem at the Vulcan plant in Caithness, which tests submarine reactors for the Ministry of Defence (MoD), occurred in January 2012. But the first the public and Scottish ministers knew about it was when Hammond made a statement in the House of Commons on Thursday.
He told MPs there had been "no measurable change in the radiation discharge" from the site. "That is the important point for people living in those communities," he said.
Radioactivity had leaked into the reactor's cooling water but had been contained within the sealed reactor circuit, Hammond said. "I can reassure the House that there has been no detectable radiation leak from that sealed circuit."
But according to the Scottish Environment Protection Agency (Sepa), discharges of radioactive noble gases including argon, krypton and xenon had been boosted by the incident. Official figures show that emissions of the gases to the atmosphere rocketed from 0.19 gigabecquerels of radioactivity in 2011 to 2.16 Gbq in 2012.
"What a tangled web Hammond weaves when he practices to deceive," Salmond told the Sunday Herald. "The emissions were indeed measurable and they were measured by Sepa."
The emissions were within the authorised limits, but they should still have been reported to the public, the First Minister said. He accused the MoD of using its Crown immunity from regulation to "gag" Sepa.
According to Hammond, Sepa was only told of the problem nine months after it was discovered. Then Sepa said it was asked by the MoD to keep the matter secret "on a strict need-to-know basis for security reasons".
Salmond said: "This is a flagrant abuse of Crown immunity, and shows total contempt for parliament and subverts the democratic accountability of Scotland."
He said ministers would be making a special statement to the Scottish Parliament on Tuesday "on what is to be done to bring the arrogance of the MoD to democratic account".
Salmond has also accused David Cameron of having "completely disrespected the Scottish Parliament and the people of Scotland, as well as the democratic processes of the whole United Kingdom".
In a letter to the Prime Minister this weekend, the First Minister argued that the UK Government had failed to live up to its promises of responsibility and trust.
"Lack of concern in such sensitive matters, especially those of such concern to the public, is as underhand as it is disrespectful," he wrote.
"You must now offer an immediate explanation of why your government allowed this to happen, an apology for the disregard of established processes and a commitment that it will never happen again."
The MoD yesterday denied that Hammond had misled parliament. The emissions Sepa was referring to were not leaks but "planned discharges" resulting from sampling to monitor reactor safety, it said.
"It is wholly misleading to confuse a planned and deliberate gaseous discharge that is well within safe levels to monitor cooling water, which the Sepa figures relate to, with a leak," stated an MoD spokeswoman. "The Defence Secretary has been clear that there has been no leak, that workers remain safe and the local community is not at risk."
According to Sepa figures, emissions of radioactive gases from Vulcan reached 43% of the authorised limit in 2012, compared with less than 4% in 2011.
"There was a discharge of noble gases to the environment as a result of the increased radioactivity within the Vulcan naval reactor," said a Sepa spokesman.
Anti-nuclear and environmental groups backed Salmond's accusations.
"Philip Hammond was clearly deceiving the House of Commons and the public," said John Ainslie, co-ordinator of the Scottish Campaign for Nuclear Disarmament. "The MoD set out to deliberately conceal this incident from the Scottish public and our government."
Richard Dixon, director of Friends of the Earth Scotland, said: "Philip Hammond categorically stated that no radioactivity was released to the environment, and we now know that this is definitely not true. Either the MoD misled him or he misled the House of Commons. Either way, someone should be losing their job."
The Sunday Herald has also discovered that the UK Government's Office for Nuclear Regulation (ONR) was not informed of the problem at Vulcan until the summer of 2012, several months after it happened. "We were required to keep the information on a need-to-know basis for security reasons," an ONR spokesman said.
The Vulcan reactor is used to test for potential problems with the reactors that drive the UK's submarine fleet, including those that carry Trident nuclear missiles. The discovery of the leak has prompted a £270 million rethink of the MoD's nuclear submarine programme.
According to Hammond, the incident resulted in the Vulcan reactor being shut down for a period in 2012. But it was of "no safety significance", he said.
However, a former senior MoD safety official pointed out that the Ministry had not yet determined the cause of the cooling water contamination.
"This being the case I have difficulty in believing their words of reassurance," said Fred Dawson, who worked for the MoD for 31 years before he retired as head of the radiation protection policy team in 2009. "If the leak is so insignificant and of no safety concern, why is the MoD planning early replacement of submarine reactor cores?"