US Admiral Jonathan Greenert (L), Chief of US Naval Operations, US Secretary of the Navy Ray Mabus (C) and US General James Amos, Commandant of the US Marine Corps, testify on the Defense Authorization Request for the fiscal year 2014 budget during a US Senate Armed Services Committee hearing on Capitol Hill in Washington, DC, on April 25, 2013. (SAUL LOEB/AFP/GETTY IMAGES)

Defense Secretary Chuck Hagel is worried about the Pentagon budget, but there are much more serious issues he must deal with. Religious proselytizing and sexual assault are at the top of the list.

In late March, as reported in the New York Times, Hagel held a conversation with a group of sergeants and petty officers who were concerned about military issues. He told them, “Remember, you always have a friend in the secretary of defense.”

Now is the time for Hagel to step to the plate and prove that friendship by eliminating all discrimination in the military.

“The armed forces are on the verge of falling apart,” Larry Wilkerson, former chief of staff to Colin Powell, told me in an interview. Aside from proselytizing, he said, other problems include “sexual assault, suicides, lowering entrance standards and war weariness. They are in trouble, and the leadership is oblivious.” Sexual assault and proselytizing, according to Wilkerson, “are absolutely destructive of the bonds that keep soldiers together.”

Wilkerson was speaking to me in an interview with former ambassador Joe Wilson and the head of the private Military Religious Freedom Foundation, Mikey Weinstein. They were on their way to a meeting at the Pentagon on April 23 where they would discuss religious issues in a group that included several generals and a military chaplain.

The chaplain’s role, according to Wilson, “is to minister to spiritual needs. You don’t proselytize. It’s a workplace violation.”

Weinstein told me after the Pentagon meeting that military leaders need to understand that “there is systematic misogyny, anti-Semitism and Islamophobia in the military.” He said it is all part of the same culture.

“This is a national security threat. What is happening [aside from sexual assault] is spiritual rape. And what the Pentagon needs to understand is that it is sedition and treason. It should be punished.”

“The chain of command is compliant,” said Wilkerson. “Abuse of power is inimical to all military. Condoning of sexual assault or proselytizing is an abuse of command.” The idea of “zero tolerance,” he said, is “the most mocked phrase in the military. It camouflages a lot.”

The proselytizing they referred to is primarily from “dominionist” or fundamentalist evangelical Christians. Weinstein’s organization has 33,000 clients, and 96 percent are Christian. These clients come to him to complain about having their religious freedom undermined in some way.

The most recent outrage, he said, was reported by a West Point cadet who wrote to Weinstein to say that after the Boston bombings, an active-duty instructor said in class that he would “bet his life on the Muslims having been behind it like they always are. It’s always the Muslims and everyone knows it, and everybody is afraid to say it. Well, I am not.”

That’s just one or many complaints.

●Recently, an Army commander in Europe overturned a jury’s conviction of an officer for sexual assault, despite the fact that the decision was unanimous.

●So called “Jesus rifles,” with gun sights inscribed with Bible quotations, were used in battle by troops. The MRFF fought successfully to have the New Testament passages removed.

●Last year, Marine officers at a U.S. base changed the name of their fighter attack squadron from “Werewolves” to “Crusaders,” with a cross and shield as an insignia. MRFF fought the change after receiving many complaints from Marines. MRFF won, and the squadron is back to Werewolves.

●A chaplain in Afghanistan recently was the target of complaint for sermonizing to troops, including Afghan soldiers, that they had approximately 2,000 days to live and needed to “get right with Jesus.”

●Weinstein even got the military to force an officer to remove an atheist bumper sticker from his car. An evangelical Christian complained about the sticker, which bore a drawing of Satan and a Christian fish.

The stories are legion. Most complainants don’t want to be identified for fear their careers would be destroyed or, worse, for fear for their safety, even their lives.

Weinstein himself once received a letter from the wife of an Air Force sniper who told him her Bible group prayed every day for him to end up in hell on fire and screaming with his friends, “the homos, the muslems [sic] the communists and the leftists. And the gun lovers and the abortionists.”

After demands from Weinstein, the Air Forced published, but has yet to distribute, a 27- page document, which includes a cover sheet that states: “COMPLIANCE WITH THIS PUBLICATION IS MANDATORY.”

“Leaders at all levels,” the document says, “must avoid the actual or apparent use of their position to promote their personal religious beliefs to their subordinates or to extend preferential treatment for any religion.” It even suggested that noncompliance could result in court-martial.

According to Weinstein, this has not been backed up.

“You need half a dozen court-martials real quick,” Wilson said.

Meanwhile, the complaints continue.

What must stop is the concept that America needs to conquer the world for Christ. An example that Weinstein gave: The Officers Christian Fellowship, in a posting on the Naval Academy’s Web site, promoted the idea of Christian officers exercising biblical leadership to raise up godly military ambassadors for Christ in uniform empowered by the Holy Spirit. “They are trying to create a spiritually transformed U.S. military,” said Weinstein.

The offensive passage was taken down after he complained, Weinstein said.

At the meeting at the Pentagon, according to Weinstein, Air Force Lt. Gen. Richard C. Harding said the instruction booklet, scheduled to be released in a few weeks as a blue pamphlet, will be a panacea to all religious issues.

Weinstein’s reaction? “I said that I don’t want to hear about blue books. What is stopping Secretary Hagel from putting out a letter that this kind of behavior will not be tolerated? Where are the commanders? And [an announcement] that the moment someone goes against the ruling they will immediately be court-martialed?”

The meeting ended on a positive note, according to Weinstein. “I said, ‘What is needed gentlemen, is leadership.’ ”

Which brings us back to Hagel telling that group that they would always “have a friend in the secretary of defense.”

Prove it.