The signatures were collected after the US branch of the charity handed Blair its "Global Legacy Award" in New York last week, The Guardian newspaper said today.
The internal letter, seen by AFP, said his history as the prime minister who took Britain into the Iraq war risks damaging Save the Children's credibility.
"The decision to award an extremely divisive figure accused of war crimes is not only morally reprehensible, but also endangers our credibility globally and could put our programmes and staff on the field at risk," it said.
The Labour leader was prime minister between 1997 and 2007, during which he led Britain into the wars in Iraq and Afghanistan and worked with the United States in the "war on terror".
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"His 'legacy' in Iraq overshadows his achievements in Africa," said the petition on 38degrees.Org.Uk.
Save the Children granted the award for Blair's role in leading G8 leaders to agree a huge package of debt relief at the 2005 Gleneagles summit and his continued work in Africa through his Africa Governance Initiative.
However, Blair's office condemned The Guardian's report of the backlash as "neither balanced nor fair".
It "conveniently disregards the facts that support the award as well as quotes from African presidents, the head of USAID and indeed anything which would give a more balanced view than the one presented", it said in a statement.