But Estrada said he will defer his "spiritual healing" to instead testify in a Senate committee inquiry on a controversial government contract awarded to an Argentine power firm in the early months of his presidency.
The court had no immediate comment on Estradas change of plan.
Estrada has been suffering from gout and eye problems and had asked the Sandiganbayan to travel to the Mother Ignacia Healing Center in Caloocan City to bathe in its spring water.
The court hearing his case said Estrada may on Monday leave the Veterans Memorial Medical Center military hospital in Quezon City where he is being detained to visit the fountain for "humanitarian reasons."
Malacañang said it respects the courts decision.
The court said the move could not be deemed a violation of a constitutional provision that says the law must apply equally to all.
It noted it had allowed Estrada in the past to undergo medical treatment at a Manila eye center.
In granting Estrada the rare privilege to leave detention "the court merely concedes considerations befitting a former highest official of the land."
"After much reflection of the issue at hand, the court is of the considered opinion that, for humanitarian reasons, the instant plea of the accused-movant can be granted," the court said.
However, Estrada said he will attend a Senate committee hearing on a government contract awarded to Argentine power firm Industrias Metalurgicas Pescarmona Sociedad Anonima (IMPSA).
It was alleged that IMPSA bagged the contract in exchange for bribes.
Estrada had maintained that he did not approve the contract, which, according to him, was concluded during the administration of his predecessor Fidel Ramos.
"National interest transcends my personal needs. Despite the lingering pain in my knees, I have decided to re-schedule my visit to the Mother Ignacia Healing Center so I can prepare for my Senate appearance," Estrada said in a statement. "I am prepared to suffer. I know what they (those who toppled him) did to me is political in nature."
Deputy Director General Edgar Aglipay, director of operations of the Philippine National Police, said they will throw a massive security blanket with air support to protect Estrada and keep out trouble.
"The PNP will spend a large amount of money on this," Aglipay said, adding that riot police will be put on standby and even traffic may be rerouted.
"In addition to this, we have directed our air support group to see to it that air support to the ground elements during his travel and even during his time of healing will be provided."
Aglipay has advised the public especially pro and anti-Estrada groups to respect police security arrangements to maintain order.
The decision by the Sandiganbayan comes amid mounting calls from politicians and influential church leaders to allow Estrada to spend Christmas with his family as a prelude to putting him under "house arrest."
While the Department of Justice has opposed the idea, spokesmen for President Arroyo said she would not oppose a house arrest for Estrada if the Sandiganbayan so decides.
Critics condemned the suggestion as a "shameless betrayal" of the Filipino people by the Arroyo administration.
Estrada said fears by prosecutors that he would escape once given a Christmas furlough were unfounded. "Escaping is farthest from my mind," he said.
Estradas lawyers on Wednesday formally filed a petition for "house arrest" with the Sandiganbayan on humanitarian grounds. A favorable decision could "soothe and allay the current political tension" between anti and pro-Estrada forces, the defense said.
"Viewed from another angle, the favorable consideration of the instant motion will be a rare exercise of a high level of judicial statesmanship by the court for healing the wounds of the past." With AFP, Christina Mendez, Marichu Villanueva