The Pentagon’s general counsel warned Tuesday against the “over-militarization” of the country’s approach to counterterrorism and said Congress should avoid micro-managing how terrorist suspects are detained and prosecuted.

“There is risk in permitting and expecting the U.S. military to extend its powerful reach into areas traditionally reserved for civilian law enforcement in this country,” Jeh Johnson said in a speech at the Heritage Foundation. “The military should not and cannot be the only answer.”

Johnson in particular criticized a series of detention provisions in the House and Senate versions of the 2012 National Defense Authorization Act.

One measure in the Senate version of the bill would mandate the military custody of any member of al-Qaeda or an affiliated organization, or anyone involved in planning an attack on the United States. It would not apply to U.S. citizens. The provision is not limited to people captured overseas, and Johnson said it could force federal law enforcement officials to turn over suspects to the military.

Johnson questioned whether the FBI or other federal agencies would have to curtail investigations or interviews to “call the Army to take the suspect away.” And he cautioned that when “we attempt to extend the reach of the military onto U.S. soil, the courts resist, consistent with our core values and our heritage.”

Republicans said this week that the detention provisions will remain in the Senate version of the National Defense Authorization Act. They noted that the measure has bipartisan support, with most Senate Democrats backing it in committee.

“We’re not going to change this bill,” Sen. Lindsey O. Graham (R-S.C.) said on Tuesday.

Johnson objected to a provision in the House version that would force the prosecution of a number of terrorist offenses in military commissions rather than in federal courts.

“Decisions about the most appropriate forum in which to prosecute a terrorist should be left, case by case, to prosecutors and national security professionals,” he said. “A flat legislative ban on the use of one system — whether it is commissions or the civilian courts — in favor of the other is not the answer.”

Johnson said that the Obama administration remains committed to closing the military detention center at Guantanamo Bay, Cuba, and that it is “firm policy” not to bring any more detainees to the U.S. military prison. The facility now houses 171 detainees.

The administration’s efforts to repatriate or resettle detainees in third countries have ground to a halt. Although dozens were slated for transfer, no one had left the facility in a year because of what Johnson called “rigid” reporting requirements imposed by Congress.

“After living with it now for almost a year, I will tell you that this provision is onerous and near impossible to satisfy,” he said.

After his speech, Johnson was asked about the lethal targeting of U.S. citizens. He replied that, in general, “those who are part of the congressionally declared enemy do not have immunity if they are U.S. citizens.”

Three U.S. citizens — including the al-Qaeda operative Anwar al-Awlaki and, in a separate strike, his 16-year-old son — have been killed in Yemen in the past few weeks.

Johnson said that “there are special considerations when it comes to U.S. citizens and particular care that should be taken.”

Bipartisan calls have been made for the Obama administration to release its legal analysis justifying the targeting of a U.S. citizen. Johnson said he thinks that “at some point” the administration will have more to say on the subject.