(Adds U.S. intelligence official's comments, other details)
By Arshad Mohammed and Andrew Quinn
WASHINGTON, July 24 (Reuters) - Syrian rebels will eventually control swathes of territory but Syrian President Bashar al-Assad still has time to negotiate an exit, U.S. Secretary of State Hillary Clinton said on Tuesday.
Speaking as if a rebel military victory was inevitable, though other U.S. officials say the 17-month armed conflict may drag on, Clinton for the first time said the opposition would ultimately be able to provide "safe haven" inside Syria.
Suggesting the U.S. focus has moved to how to grapple with an eventual collapse of Assad's rule, Clinton stressed it was time to look at "day-after issues" such as how to govern a post-Assad Syria and how to avert a bloodbath of sectarian reprisals.
The last week appears to have been the bloodiest in the conflict in which the Alawite minority that has ruled the Sunni majority country for four decades has sought to crush the rebels' uprising against Assad.
"We have to work closely with the opposition because more and more territory is being taken and it will, eventually, result in a safe haven inside Syria which will then provide a base for further actions by the opposition," Clinton said at a news conference with Haitian Prime Minister Laurent Lamothe.
"We do believe that it is not too late for the Assad regime to commence with planning for a transition, to find a way that ends the violence by beginning the kind of serious discussions that have not occurred to date," Clinton said.
Clinton made no suggestion that the U.S. government would help defend any rebel safe havens against Damascus' heavy weaponry, which would require a major escalation of Washington's involvement in the conflict.
She said that among the challenges the opposition must prepare for are creating governing entities, protecting Syria's chemical weapons, facilitating humanitarian relief and protecting the rights of all Syrians should Assad fall.
"It's important to look at these day-after issues," Clinton said.
"We're working across many of these important pillars of a transition that is inevitable. It would be better if it happened sooner both because fewer people would die or be injured, but also because it would perhaps prevent sectarian retribution," she added.
U.S. INTELLIGENCE SEES PROTRACTED CONFLICT
Syrian troops backed by helicopter gunships fought rebels trying to seize central Aleppo and pursued a campaign to regain full control of the capital Damascus, residents and opposition activists said.
U.S. intelligence officials see both sides in Syria as being in it for the long haul and that while the opposition since April has begun to be more effective against the Syrian government, the likelihood remains for a protracted conflict.
U.S. intelligence officials say the overall trend for Assad's government continues to be downward.
Earlier in a speech at the U.S. Holocaust Memorial Museum, Clinton said the Obama administration - which has previously said that it is providing communications equipment to the rebels - was now doing more, though she did not provide details.
"I have to say that we are also increasing our efforts to assist the opposition," Clinton said.
"It will be unfortunate if, indeed, the Assad regime and those around them decide that it's an existential struggle for them and they will maintain and even increase the level of violent response," she added.
Clinton later told reporters that the "existential struggle" comment was meant both to signal to the rebels that they should not pursue reprisals against the Alawite minority as well as to make clear to Assad that he could still negotiate an exit.
"Those are two good options," Clinton said. "We do believe that it is not too late for the Assad regime to commence with planning for a transition, to find a way that ends the violence by beginning the kind of serious discussions that have not occurred to date.
"It's very important that the opposition fighters, as they get better organized and expand their presence more broadly, send a message that this is for the benefit of all Syrians, not for any group, not engage in any reprisals and retribution that could lead to even greater violence," she added. (Additional reporting by Khaled Yacoub Oweis in Amman and Tabassum Zakaria in Washington; Editing by David Brunnstrom, Cynthia Osterman and Jackie Frank)