It said the North was deliberately misinterpreting Seoul's objectives and remarks by its officials.
"Our side has sincerely upheld the non-aggression agreement between the South and the North, and this position will not change in the future," Major-General Kwon Oh-sung, Seoul's chief delegate to the military dialogue, said in the message.
North Korean state media on Monday published a sharp rebuke of Lee, calling him a "conservative political charlatan" and accusing him of being a US sycophant and a traitor.
February 25 Lee Myung-bak takes office as South Korean president. Promises to end unconditional aid to North, saying Pyongyang must improve human rights and return Southerners held since the 1950-53 Korean War
March 26 South Korean military chief tells MPs military will strike suspected nuclear weapons site in North if Pyongyang attempts to attack South with atomic bombs
South Korean foreign ministry says it will back a UN resolution condemning North's human rights record, ending a decade of reluctance by previous administrations
March 27 Pyongyang expels South Koreans working at joint industrial zone in the North
March 28 North Korea test-fires missiles into sea and warns it will "mercilessly wipe out" any South Korean warships that violate its waters
March 29 North warns inter-Korean reconciliation may be in jeopardy, implements ban on South Korean officials entering the country
March 31 North Korea threatens to turn the South to "ashes" after South's warning of pre-emptive strike in response to nuclear attack
April 1 North accuses South Korean president of being US stooge and causing instability on peninsula
April 2 South's defence ministry tells North to stop verbal attacks in first official response
Timeline: The Two Koreas
In its commentary, the Rodong Sinmun
described Lee's policy towards the North as a "declaration of war", warning that he was "making a mess of the process to denuclearise the peninsula".
"Lee's seizure of power created a thorn bush in the way of the inter-Korean relations", it said, warning against misjudging "the patience and silence so far kept by" the North.
The escalating war of words have stoked tensions on the Korean peninsula.
Daniel Pinkston, a North Korea watcher, told Al Jazeera the North may be taking the opportunity to try to influence parliamentary elections that the South will hold on next week.
Aside from the barbed rhetoric, recent days have also been marked by Pyongyang test-firing missiles, ejecting South Korean officials from a shared industrial zone, and accusing South Korean ships of breaching a disputed sea border last week.
On Sunday, the North threatened to turn its neighbour to "ashes" after South Korea's military chief said he would consider of a pre-emptive strike if the military believed North Korea was preparing a nuclear attack.
Lee, who pledged a tougher line on ties with the North, has said that South Korean aid to the impoverished North will no longer be given unconditionally.
In a marked change from previous administrations he has also said that his government will not shy from criticising Pyongyang's human-rights abuses.
Lee's conservative Grand National Party, responding late on Monday to the "ashes" threat, called on the North to stop "blackmailing" the South.
"We should face North Korea's military threat dauntlessly and resolutely," the party said in a statement.
On Monday the US state department expressed concern over the increasing hostility between the two Koreas, saying the harsh rhetoric was not helping the much-delayed six-nation nuclear disarmament talks.
The US urged North Korea on Wednesday to end the three-month stalemate in nuclear talks within the next few days.
Christopher Hill, the chief US nuclear negotiator, said in Seoul that differences over Pyongyang's promised nuclear declaration had narrowed but time was running out.
"We are very concerned that we really needed this to wrap up by the end of March. Here it is already after the end of March," Hill said after talks with senior South Korean officials on ways to get the negotiations moving.
While some differences on the declaration had narrowed, Hill said "whether they are significant we won't know until we actually have a declaration".
"So we'll have to see whether we can hear anything new from the DPRK on this, really in the next few days," he said, referring to the Democratic People's Republic of Korea, the North's official name.
A 2007 six-nation denuclearisation deal, involving China, the two Koreas, Japan, the US and Russia, offers the North energy aid and diplomatic and security benefits in return for full denuclearisation.
But it has stalled over the declaration, which was due to be handed over by the end of last year and should list all of Pyongyang's nuclear activities.
The North says it submitted the document last November but the US says it has not fully accounted for a suspected secret uranium enrichment weapons programme or for alleged nuclear proliferation to Syria.
According to a report in South Korea's Chosun Ilbo newspaper on Tuesday, Hill recently confronted North Korean officials with US evidence of North Korea's alleged nuclear links with Syria.
Hill presented Kim Kye-gwan, the North's nuclear envoy, with a list of officials and engineers said to be involved in the technology transfer, but Chosun Ilbo did not say where the meeting took place.