WASHINGTON — As prosecutors put the finishing touches on the 2008 indictment of Blackwater security contractors for a deadly shooting in Iraq, the F.B.I. agents leading the investigation became convinced that political appointees in the Justice Department were intentionally undermining the case, internal emails show.

The F.B.I. had wanted to charge the American contractors with the type of manslaughter, attempted manslaughter and weapons charges that could send them to prison for the rest of their lives for the shooting, which left more than a dozen Iraqis dead and many others wounded in September 2007.

But at the last minute, the Justice Department balked. In particular, senior officials were uncomfortable with bringing two machine-gun charges, each of which carried mandatory 30-year prison sentences.

“We are getting some serious resistance from our office to charging the defendants with mandatory minimum time,” Kenneth Kohl, a federal prosecutor, told the lead F.B.I. agent on the case, John Patarini, as the Justice Department prepared to ask a grand jury to vote on an indictment in December 2008.