Fowler, the highest-ranking UN official in Niger, and his colleague Louis Guay, were kidnapped and held for four months before being released in April 2009.
In a book he later published, Fowler said he did not know if a ransom was paid.
The Associated Press says it found the al-Qaida letter mentioning the ransom inside a building formerly occupied by the group's fighters in Mali.
The letter was sent by al-Qaida's North African branch to Moktar Belmoktar, who split from the group to conduct his own operations, including the Fowler kidnapping in December 2008.
The letter said that a plan to force concessions in the U.S.-led war in Afghanistan was stymied when Belmoktar struck his own deal for about $1 million for both men.
"Rather than walking alongside us in the plan we outlined, he managed the case as he liked," the al-Qaida leaders write indignantly.
After setting up his own group, Belmoktar mastermined two operations that killed 101 people in all _ at an Algerian gas plant in January and simultaneous bombings at a military base and a French uranium mine in Niger last week.
Among other things, the letter reveals, the leaders of al-Qaida's North African branch criticized Belmoktar for failing to answer his phone when they called, failed to turn in expense reports, ignored meetings and refused to carry out orders.
The letter, signed by the group's 14-member governing body, describes its relationship with Belmoktar as "a bleeding wound."
The Associated Press report does not indicate who paid the ransom for Fowler and Guay.
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