In a statement issued today, Ms Higgins said the letter was written in a “personal capacity”.
Ms Higgins said she put the letter on her dedicated section on the President’s official website so that people could access it.
However, she said she soon took it down when she saw it “being presented as not being from myself, but from the general President.ie website".
“For the last 11 years since coming to Áras an Uachtaráin as the wife of the President, I have continued my long standing interests on a number of important issues," she said.
"Since 2014, I have had a dedicated section on the President.ie website. This section contains details of activities I have been undertaking including speeches and work towards the implementation of the United Nations’ Sustainable Development Goals, health issues, breastfeeding, issues affecting the Traveller Community, human rights, supporting the arts and a range of other issues.
“Last week I had been asked about my letter to the Irish Times, which I had written in a personal capacity, by a number of people who had missed it, and had not been able to access it online.
"I therefore put it on my dedicated section of the website as I have done for the last number of years. Having put my letter up, I subsequently took it down when I saw it being presented as not being from myself, but from the general President.ie website.
“I have from its outset strongly condemned the illegal Russian invasion of Ukraine and I cannot be but dismayed that people would find anything unacceptable in a plea for peace and negotiations when the future of humanity is threatened by war, global warming and famine.”
It follows days of mounting pressure over the letter commenting on Russia’s invasion of Ukraine.
In the letter, Mrs Higgins said the fighting would go on until the world "persuades President Vladimir Putin of Russia and President Volodymyr Zelensky of Ukraine to agree to a ceasefire and negotiations".
In response to Ms Higgins’ statement today, Senator Gerard Craughwell said the President’s official website is “there for the constitutional holder of the office”.
“I note that Mrs Higgins had issued a statement regarding the publication of her letter to the Irish Times on the President’s website,” he said.
“I can see no justification for any private citizen having a dedicated section of that website. We need to clarify the role (if any) of the spouse or partner of any sitting president. We still need to hear from the President himself.”
Speaking on RTÉ’s Drivetime programme this evening, Fianna Fáil senator Malcolm Byrne welcomed Ms Higgins’ statement but said he did not feel the need to apologise for his previous criticism of the letter.
Senator Byrne said today’s statement “provides clarity” but it is “unfortunate” that it was not issued earlier.
“I welcome the intervention of Mrs Higgins, she’s a woman I have enormous respect for, and I think this certainly does bring some clarity to the matter,” he said.
“I think it makes very clear that she does regard Russia as the aggressor and certainly I think she would regret the fact that the Russia ambassador in the Kremlin would have used her letter as a propaganda tool.
“I disagreed with her views, there were a couple of elements, first of all within the letter, it seemed to imply that there was a moral equivalence between the actions of Russia and those of Ukraine.
“The second issue then was that it did appear on the Presidential website, and I get the point that’s being made but this was very clearly a political statement that was made.
“The letter was endorsed by the Russian ambassador, and it caused offense to a lot of Ukrainians.”
On Saturday, Senator Byrne said Ms Higgins was “entitled to her personal opinion” but that he believed she was “totally wrong to try to see an equivalence in the positions of Ukraine and Russia”.
“The decision to publish the letter on the president’s website raises serious questions,” he said.
“It is incumbent on the president of Ireland to now express clearly the strong support of the people of Ireland for the people of Ukraine and that we hold Russia responsible for the war and ongoing barbarism.”
Louth Fianna Fáil Senator Erin McGreehan earlier today said the President had “disrespected” Ireland and should “at least” apologise.
“An Uachtaráin disrespected our nation and the Office of the Presidency when he published his wife’s letter - At least [sic] he needs to apologise and if he doesn’t he should most definitely consider his position,” she said.