BAGHDAD, Iraq (CNN) -- U.S. troops in Iraq will gradually reduce their visibility after a new security pact takes effect, but they won't lose the "fundamental ability to protect" themselves, the top U.S. general in Iraq said Friday.
Shiite Muslims burn a replica of the American flag in the Sadr City district of Baghdad on Friday.
Troops should prepare for "a subtle shift" in the way they operate -- as all missions will need approval from the Iraqi government under a security agreement that takes effect at the end of the year, Gen. Ray Odierno told his forces Friday.
In a letter to U.S. military personnel, Odierno says they must "steadily reduce our visibility," but the new rules of engagement will not mean "any reduction in our fundamental ability to protect ourselves."
The security pact sets June 30, 2009, as the deadline for U.S. combat troops to withdraw from all Iraqi cities and towns. Under the agreement, the date for all U.S. troops to leave Iraq is December 31, 2011.
"Despite some adjustments to the way we conduct operations, the agreement simply reinforces transitions that are already underway, and I want to emphasize that our overarching principles remain the same," Odierno wrote.
Iraq's presidency council Thursday approved the U.S.-Iraq security agreement -- the final step for the agreement to be ratified by the Iraqi government, according to presidency council spokesman Nasir Al-Ani. The pact allows the presence of American troops in Iraq for three more years.
"As we prepare for operations under the new agreement, we do so with an understanding that our mission, objectives, and commitment to the Iraqi people remain unchanged," Odierno wrote. "The new environment, though, will require a subtle shift in how we plan, coordinate, and execute missions throughout Iraq."
U.S. troops will still engage in combat, he wrote, but "we will coordinate and execute those operations with the approval of the GoI (Government of Iraq), and we will conduct all operations by, with, and through the Iraqi Security Forces."
"Similarly, we will continue to focus on combating al Qaeda and other extremist groups, but we must do so with respect for the Iraqi Constitution and laws, and we must continue to treat all Iraqi citizens with the utmost dignity and honor," Odierno wrote.
A field manual used by American troops -- known as Tactics, Techniques and Procedures (TTPs) -- will be updated to reflect the new rules of engagement, "but there will not be any reduction in our fundamental ability to protect ourselves and the force."
"While we must remain adaptive and steadily reduce our visibility, we must also maintain our effectiveness in accomplishing our objectives," he told the roughly 140,000 troops under his command.
The three-member presidency council, which consists of President Jalal Talabani, Shiite Vice President Adel Abdul Mehdi and Sunni Vice President Tariq al-Hashimi, approved the agreement unanimously a week after the Iraqi parliament passed the measure. Under the Iraqi constitution, unanimous approval by the presidency council is required for ratification of a law or agreement.
The security pact, which is to replace a United Nations mandate for the U.S. presence in Iraq that expires at the end of year, was reached after months of negotiations between Iraqi and U.S. representatives.
Stressing respect for Iraqi sovereignty, the pact "requests the temporary assistance" of U.S. forces, but severely restricts their role. It states that all military operations are to be carried out with the agreement of Iraq and must be "fully coordinated" with Iraqis.
A Joint Military Operations Coordination Committee will oversee military operations.
Iraq has the "primary right to exercise jurisdiction" over U.S. forces "for grave premeditated felonies," the agreement reads. Suspects can be held by U.S. forces but must be available to Iraqi authorities for investigation or trial.
Iraq also will have the "primary right to exercise jurisdiction" over U.S. contractors and their employees under the agreement. The pact also states that "Iraqi land, sea and air shouldn't be used as a launching or transit point for attacks against other countries."
The presidency council also approved a U.S.-Iraqi bilateral pact called the strategic framework agreement, which covers a wide range of bilateral cooperation efforts and which was approved by the Iraqi parliament last week.
Odierno and U.S. Ambassador to Iraq Ryan Crocker issued a statement welcoming the council's ratification of the measures.
"We look forward, under these agreements, to the continued reduction in U.S. forces and the normalization of bilateral relations as two sovereign and co-equal nations," they said.
"We will undertake initiatives to strengthen our cooperation in the fields of economics, energy, health, the environment, education, culture, and law enforcement. The United States will support Iraq's request to the U.N. Security Council to continue protection of Iraqi assets," the statement said.