Fake mobile phone towers, often called Stingrays, offer valuable information about suspects but also collect vast amounts of data from innocent passers-by.
From now on, agencies will need to obtain a search warrant to use such devices.
The US Department of Justice said it wanted to protect citizens' privacy.
"Cell-site simulator technology has been instrumental in aiding law enforcement in a broad array of investigations, including kidnappings, fugitive investigations and complicated narcotic cases," Deputy Attorney General Sally Quillian Yates said in a statement.
"This new policy ensures our protocols for this technology are consistent, well-managed and respectful of individuals' privacy and civil liberties," she added.
The policy, which takes effect immediately, applies to the Federal Bureau of Investigation (FBI)  the Bureau of Alcohol, Tobacco and Firearms, the Drug Enforcement Administration (DEA) and the United States Marshals Service.
It does not apply to local police forces although some states, including Washington, Virginia, Minnesota and Utah, have already imposed a warrant requirement.
The portable boxes can be used to determine the location of a suspect and can also intercept calls and text messages.
The American Civil Liberties Union (ACLU) estimates that up to 53 agencies in 21 states own Stingrays.
It has long complained that the use of the technology is shrouded in secrecy, making it hard to accurately pinpoint how widely they are used.
ACLU lawyers welcomed the move but said that more could be done to extend the policy to all law enforcement agencies.
It also pointed out that there were several loopholes in the legislation that allowed law enforcers to use the technology without a warrant.
Earlier this year, German security firm GSMK Cryptophone claimed to have uncovered evidence of at least 20 instances of the use of cell-site simulators in the UK.
The Metropolitan Police Service refused to confirm or deny it was using them.
The US government is cracking down on the way law enforcement agencies use technology to track criminals.