The al-Qaeda chief, killed in a US raid a year ago, underscores "the need to cancel other attacks due to the possible and unnecessary civilian casualties" in Muslim countries, according to the letter.
"We ask every emir in the regions to be extremely keen and focused on controlling the military work," he wrote, referring to al-Qaeda attacks.
Bin Laden expressed concern about his network losing the sympathy of Muslims and described operations killing Muslims as "mistakes", adding that was important that "no Muslims fall victim except when it is absolutely essential."
"It would lead us to winning several battles while losing the war at the end," he wrote.
The letter was among 17 declassified documents that the White House allowed to be published online by the Combating Terrorism Center at the West Point military academy.
The papers include letters or draft letters dated from September 2006 to April 2011, a total of 175 pages in the original Arabic.