Colleen Graffy told the BBC the deaths were part of a strategy and “a tactic to further the jihadi cause”, but taking their own lives was unnecessary.
“I would not say that it was a PR stunt,” said spokesman Sean McCormack.
Meanwhile, a US lawyer has said that one of three who killed themselves was due to be freed but did not know it.
Mark Denbeaux, who represents some of the foreign detainees at the US camp in Cuba, said the man was among 141 prisoners due for release.
He said the prisoner was not told because US officials had not decided which country he would be sent to.
On Sunday Deputy Assistant Secretary of State for Public Diplomacy Ms Graffy told the BBC’s Newshour programme the three men did not value their lives, nor the lives of those around them.
Detainees had access to lawyers, received mail and had the ability to write to families, so had other means of making protests, she said, and it was hard to see why the men had not protested about their situation.
When asked about the comments, the state department spokesman said the US had serious concerns whenever someone took their own life.
Mr McCormack would not comment on whether Ms Graffy had been rebuked for her remarks.
Camp commander Rear Adm Harry Harris has also taken a tough line on the suicides, saying it was an “act of asymmetric warfare waged against us”.
The Pentagon named the prisoner who had been recommended for transfer as 30-year-old Saudi Arabian Mani Shaman Turki al-Habardi Al-Utaybi.
He was a member of a banned Saudi militant group, the defence department said.
The other two men who died on Saturday morning were named as Ali Abdullah Ahmed, 28, from Yemen, and Yassar Talal al-Zahrani, 21, another Saudi Arabian.
Ahmed was a mid- to high-level al-Qaeda operative who had participated in a long-term hunger strike from late 2005 to May, and was “non-compliant and hostile” to guards, the Pentagon said.
Zahrani, 21, was a “front-line” Taleban fighter who helped procure weapons for use against US and coalition forces in Afghanistan, according to the department.
Lawyers say the men who hanged themselves had been driven by despair.
The prison camp at the US base in Guantanamo Bay, Cuba, holds some 460 prisoners, the vast majority without charge.
There have been dozens of suicide attempts since the camp was set up four years ago – but none successful until now.
Criticism of the camp is mounting.
The United Nations rapporteur on torture, Manfred Nowak, said European leaders should use a summit with President George W Bush next week to press for the prison’s closure.
Danish Prime Minister Anders Fogh Rasmussen said procedures at Guantanamo Bay violated the rule of law and undermined the fight against terrorism.
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