Though this week’s declaration of Mohammed Morsi as Egypt’s first freely-elected president is a significant milestone in the ancient Arab state’s history, the battle for the future of this key country isn’t over.

Actually, far from it.

Egypt is still quite divided some 16 months after former-President Hosni Mubarak ceded power to the Supreme Council of the Armed Forces (SCAF), a supposed military caretaker government, in the early days of the Arab Spring.

Morsi, the candidate of the Islamist Muslim Brotherhood, only took 52 percent of the vote of the 50 million person electorate. His opponent, Ahmed Shafik, who represented the old guard in the polls, garnered a close 48 percent.

The new president can hardly claim a mandate in the country of some 80 million.

On top of this, Morsi will also have to try to form a new government absent the Muslim Brotherhood-dominated parliament that a SCAF-friendly court recently dissolved. Without a date for new parliamentary elections, governing won’t be easy.

Just after the election, the SCAF also moved to limit presidential powers by issuing a convenient “constitutional addendum,” clipping the new chief executive’s Islamist wings before he’s had a chance to fly.

For instance, SCAF head, Field Marshal Mohammed Hussein Tantawi, now has veto power over the new constitution’s writing; authority over defense matters; and, must give the OK to Morsi on using troops for addressing internal unrest or declaring war.

And while the SCAF is scheduled to turn over power to the new civilian government on June 30, don’t hold your breath. Any real military-civilian power shift — if it happens at all — won’t take place till the ink is dry on the new constitution.

Of course, there are plenty who believe the military, which has essentially ruled the country for nearly six decades and has a lot to lose in a power transfer, will not go gently — or quietly — into that good Nile night.

Ultimately, we may see a “co-presidency” in Egypt for a bit, where the president has control over domestic matters, while the military continues its reign over national security.

Of course, the big question for the United States is how the rise of new powers (such as the Muslim Brotherhood) in Egypt will affect American interests?

It’s not clear at this point, but concerns include the future of secularism, the Camp David (Peace) Accords, ties with Iran, religious tolerance (especially treatment of the nation’s Coptic Christians), women’s rights, economic reform, Suez Canal access and Sinai security among other issues.

What is also troubling is the lack of influence Washington will have in the outcomes in Cairo, evidence, regrettably, of America’s increasingly shrinking visibility and sway in the region under Team Obama, especially since the Arab Spring “bloomed.”

Unfortunately, our diminished clout in the historic events taking place in this central Arab state will likely result in suboptimal outcomes for American leadership — and, worse yet, U.S. interests.

Peter Brookes is a Heritage Foundation senior fellow and a former deputy assistant secretary of defense.