States will be able to create systems for regulation of cannabis sales but administration reserving right to sue at later date.
The Obama administration has said it will not sue to stop the states of Colorado and Washington from allowing recreational marijuana use.
Attorney general Eric Holder told the governors of both states on Thursday that the Justice Department would allow them to create systems for the regulation of marijuana sales. The department has reserved the right to file a lawsuit against the states at a later date.
Colorado and Washington passed amendments legalising marijuana in November last year. The votes made it legal for people over 21 to possess up to one ounce of marijuana in each state, although there were some differences over the legality of growing cannabis plants.
In announcing that the government will allow Colorado and Washington to implement their marijuana laws the Justice Department introduced sweeping guidelines which outlined eight top priority areas where it said cannabis legislation must be enforced. The guidelines were issued to all US attorneys, recommending that they focus on prosecuting major cases.
The three-and-a-half page memo said that priorities for federal prosecutors should include preventing the distribution of marijuana to minors, preventing revenue from the sale of marijuana from going to criminal gangs and preventing marijuana being diverted from states where it is legal to other states where it is not.
Other measures included prosecuting people who drive under the influence of marijuana and preventing the drug from being grown on public lands.
The announcement follows comments in December by President Barack Obama, who said it does not make sense for the federal government to go after recreational drug users in a state that has legalized recreational use of small amounts of marijuana.
Colorado residents voted in favour of Amendment 64 on 6 November 2012, by 53.3% to 46.7%. The amendment allows "personal use and regulation of marijuana" for adults 21 and older and allows for the possession of up to one ounce of cannabis. The amendment also allows those 21 and above to grow up to to six marijuana plants, as long as they are in a locked space. Washington's measure No 502 affords similar liberties, although individuals 21 and over must apply for a license to grow and sell marijuana.
Obama said last year that law enforcement agencies had "bigger fish to fry" than to go after users in Washington and Colorado.
"It would not make sense for us to see a top priority as going after recreational users in states that have determined that it's legal," he said.