Iran said Mr Akhoondzadeh did not meet US officials in The Hague
Iran has denied that a meeting took place between their main representative at an international conference on Afghanistan and a senior US official.
US Secretary of State Hillary Clinton had said that Richard Holbrooke and Mohammad Mehdi Akhoondzadeh had an informal but "cordial exchange".
She said the US had given the Iranian delegates a letter, but Iran's foreign ministry "categorically" denied this.
The US had welcomed Iran's presence at the meeting as a "promising sign".
On Tuesday, Mrs Clinton said that Mr Holbrooke and Mr Akhoondzadeh had had a brief meeting on the sidelines of the conference in the Hague.
She said the meeting had been unplanned but that the men had agreed to "stay in touch".
But on Wednesday, foreign ministry spokesman Hassan Ghashghavi told Iran's Mehr news agency: "No meeting or talk, be it formal or informal, official or unofficial between Iran and US officials took place on the sideline of this conference."
"We categorically deny the reports published in this regard," he said.
Mr Ghashghavi said that as no meeting had taken place, "naturally no letter was handed to Iran from the American side".
Mrs Clinton said Iran's presence at The Hague meeting was 'a promising sign'
Mrs Clinton had said the letter was about the welfare of three US nationals in Iran.
Mrs Clinton's comments came at the end of a one-day meeting of delegates from 70 countries and other organisations interested in rebuilding Afghanistan.
It was called by the UN amid widespread concern that not enough progress has been made since the US-led invasion in 2001.
Iran's presence at the Hague had been described by Mrs Clinton as "a promising sign that there will be future co-operation".
Tehran gave a guarded welcome to US plans at the meeting to increase regional co-operation over Afghanistan.
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