Secretary of State John Kerry said Afghanistan and the United States have reached agreement on “the final language of the bilateral security agreement” to be presented to Afghan leaders Thursday. (PAUL J. RICHARDS/AFP/Getty Images)

Afghanistan and the United States have reached agreement on “the final language of the bilateral security agreement” to be presented to Afghan leaders on Thursday, Secretary of State John F. Kerry said Wednesday.

Kerry did not mention the separate “assurances” that Afghan President Hamid Karzai sought Tuesday in the form of a letter signed by President Obama. White House and State Department officials said they were “still working through” that aspect of the deal.

“It is up to the White House to address issues with respect to any possible communication” between the two leaders, Kerry said. He indicated that Karzai would present any such communication Thursday to the more than 2,500 Afghan elders and other leaders who will begin considering the agreement in Kabul.

In last-minute negotiations this week, Karzai requested a U.S. pledge that American troops would not enter the homes of Afghan civilians, as well as a statement of regret for the deaths of Afghan civilians at the hands of U.S. forces.

U.S. officials insisted overnight and Wednesday morning that any expression of regret would not constitute an “apology” by the United States. “That’s not what’s in the offing. It’s not what’s been suggested,” Benjamin Rhodes, Obama’s deputy national security adviser, told CNN. “We have, of course, throughout the war, always indicated regret when there are instances of civilian casualties.”

Kerry said final agreement on the security document, under negotiation for the past year, had been reached in a series of conversations he had with Karzai on Wednesday morning. The language, he said, will be submitted to the loya jirga, as the Afghan assembly is known.

Although the views of the jirga will be nonbinding, Karzai has said that body will decide several controversial provisions of the deal, including the granting of immunity to U.S. troops who commit crimes on Afghan soil. The agreement text grants the United States full legal jurisdiction over U.S. troops and Defense Department civilians working in Afghanistan.

The five-day jirga event is being held under tight security in a large tent at Kabul Polytechnic University. The area around the university is effectively locked down for the event, and many delegates are not identifying themselves for fear of reprisal attacks from Taliban militants.

On Wednesday, some Afghan analysts appeared bewildered by Karzai’s request for additional U.S. assurances, accusing him of unnecessarily prolonging the drama surrounding the negotiations.

“It’s just throwing dust in the eyes of the jirga,” said Waheed Mozhdah, a Kabul-based analyst and historian. “Obama is in his last term and has no way of guaranteeing the future deeds of American soldiers.”

Although the agreement does not include troop numbers, the United States is likely to keep a residual force in Afghanistan in training and support roles. Most estimates suggest that 5,000 to 10,000 troops will remain, allowing the United States to maintain a foothold in the volatile region and serve as a backstop of support for Afghan troops battling the Taliban insurgency.

There is no limit on how long U.S. forces would remain, an issue that could surface during the Afghan deliberations. U.S. officials have said the duration is indefinite, and an undated draft released Wednesday by Afghanistan’s Foreign Ministry said the U.S. presence would last to “2024 and beyond.” A separate strategic partnership agreement signed last year between the two governments is due to expire in 2024. Several Afghan legislators have said in recent days that they thought there would be a 10-year limit on the security agreement.

Hakimullah Mujahed, a member of Afghanistan’s High Peace Council who will take part in the loya jirga, said Wednesday that he will aggressively seek to remove a clause granting U.S. troops immunity for crimes committed on Afghan soil.

“It’s a big, big problem and will be the focus of the jirga,” said Mujahed, who said such immunity would violate international law. “It’s a matter of principle and a question of justice.”

He said he suspects that the gathering will amend the draft to strip out immunity, leaving it up to Karzai to decide whether to proceed without the full backing of the group. The country’s parliament also will have to approve the agreement before it can go into effect. “We still have a very long journey to go on this,” Mujahed said.

U.S. officials have said they are unlikely to keep any forces in Afghanistan without the immunity clause, resulting in a complete pullout akin to the one in Iraq in 2011 after a similar dispute.

That prospect is also weighing heavily on loya jirga delegates.

Hashmat Ghani Ahmadzai, an Afghan politician and analyst, said there was widespread concern among business leaders and residents in urban centers that a U.S. withdrawal would create a vacuum that Iran or Pakistan would fill.

“If not Americans, it has to be someone else or a neighboring group or local group,” Ahmadzai said.

Haji Amin, a money dealer who will represent the Chamber of Commerce at the jirga, said many attendees think Afghanistan needs “a big, power ally” such as the United States if it is to survive as a democracy.

“We want a similar deal with the United States like it has with Japan and South Korea,” Amin said.

The agreement draft posted online Wednesday covers a number of points known to have been agreed to earlier this month.

Dated only “November,” it says that “unless mutually agreed, United States forces shall not conduct combat operations in Afghanistan.” It states the parties’ “intention of protecting U.S. and Afghan national interests without U.S. military counter-terrorism operations” but does not specifically prohibit such operations.

In an indirect mention of the home-entry issue, it says the “goal” of such operations is to keep Afghan security forces in the lead, “with full respect for Afghan sovereignty and full regard for the safety and security of the Afghan people, including in their homes.”

It also notes that “U.S. forces shall not target Afghan civilians, including in their homes, consistent with Afghan law and United States forces’ rules of engagement.”

On troop immunity, it says that Afghanistan agrees “that the United States shall have the exclusive right to exercise jurisdiction” over members of the force and its civilian component “in respect of any criminal or civil offenses committed in the territory of Afghanistan.”

Afghan authorities are prohibited from detaining American troops or U.S. civilians working with them. In the event that happens “for any reason,” however, those personnel “shall be immediately handed over to United States forces authorities.”

The agreement also specifies that American troops and civilians cannot be surrendered to any “international tribunal or any other entity or state” without express U.S. consent. Afghanistan, it says, retains legal jurisdiction over civilian contractors, and contractors are prohibited from wearing military uniforms and “may only carry weapons in accordance with Afghan laws and regulations.”

In a preamble, the draft specifies that “the United States does not seek permanent military facilities in Afghanistan, or a presence that is a threat to Afghanistan’s neighbors, and has pledged not to use Afghan territory or facilities as a launching point for attacks on other countries.”

It says that “unless otherwise mutually agreed, United States forces shall not conduct combat operations in Afghanistan” and makes no promise of U.S. military support in the event of an attack or other security threat to Afghanistan. If there is such a threat, it says, the United States will regard it with “grave concern,” consult and “shall urgently determine support it is prepared to provide.”

The draft agreement says that U.S. military and Defense Department civilian personnel are exempt from visa requirements and taxation. Afghan taxes and other fees will not be imposed on the entry or exit of goods specifically for the use of U.S. forces.

An annex to the draft lists locations where Afghanistan agrees to provide facilities for U.S. forces, including Kabul; Bagram, north of the capital, where the United States has its largest current base; Mazar-e Sharif in northern Afghanistan; Herat in the west; Kandahar in the south; Shindand in Herat province; Sharab in Helmand province; Gardez, south of Kabul; and Jalalabad, to the east.

Craig reported from Kabul. Mohammad Sharif and Sayed Salahuddin in Kabul contributed to this report.