Many Indonesians reacted to his October offer with suspicion rather than gratitude.
Bush's move followed similar US attempts at introducing changes in the educational systems of a number of Muslim countries, including Pakistan and Saudi Arabia, since the 9/11 attacks.
He appeared to be acting on the advice of his more hawkish advisers, who aim to replace a curriculum perceived as radical and anti-American with a more compliant alternative.
“Education, both in conventional schools and pesantrens [religious schools], could prevent people from resorting to radical action. But the US must be careful not to intervene in the school curriculum,” said Hasyim Musadi, leader of the largest Muslim organisation in Indonesia, Nahdlatul Ulama.
“If the US enters into the curriculum, it can be accused of intervening in the pesantrens’ educational system,” he continued, referring to Indonesia's Islamic boarding schools.
US attention turned towards specific religious educational institutions after allegations began to surface about links between some pesantrens and the perpetrators of the Bali Bomb blast of 2002 and the Jakarta Marriot bomb blast of 2003.
Some of the key suspects of both major Indonesian bombing attacks had graduated from al-Mukmin, Ngruki, in Central Java, a school that was co-founded by Abu Bakar Ba’asyir, jailed recently after being accused of plotting to topple the government.
Bali bomber Ali Gufron studied at the al-Mukmin pesantren
“It is not fair to generalise about all pesantrens,” said Din Syamsuddin , deputy chairman of Muhammadiyah, the second largest Muslim organisation in the country, referring to the accusations that pesantrens are "terrorist incubators".
Syamsuddin also stressed the importance of remembering that thousands of other pesantrens in the country are moderate in outlook and are far from being a threat.
Musadi agreed: “If there are people saying that the system is dangerous, I will deny it. This is the best system that can address the problem that Muslims face,” he said.
In response to the local outcry, the US ambassador to Indonesia, Ralph Boyce, quickly issued a statement reassuring Indonesians that Washington did not intend to interfere in the curriculum of Islamic schools.
According to the ambassador, who in recent weeks had visited Indonesian schools donating books and promoting the education pledge, the aid “is designed to support the educational goals and priorities identified by Indonesian themselves".
“I don’t know where the idea [of the US planning to intervene in the curriculum] comes from. The education system in pesantren is one of the greatest education systems in the country,” Boyce told reporters.
“America will not interfere. America will study the system,” said Boyce, as quoted by Musadi.
But not everyone in the US government seems to think so.
Both US Secretary of Defence Donald Rumsfeld and his deputy Paul Wolfowitz have separately raised the issue of combating anti-American influence in "radical" Islamic schools.
US hawk Paul Wolfowitz says the schools' tools are all wrong
“Should we create a private foundation to entice radical madrassas [or pesantrens] to a more moderate course?” Rumsfeld wrote in a private 16 October memo quoted by the Washington Post newspaper.
On a different occasion, Paul Wolfowitz, himself a former US ambassador to Indonesia, said, “What they are taught there [madrassas/pesantrens] is not real learning. It’s not the tools for coping with the modern world. It’s the tools that turn them into terrorists.”
Despite the concerns of Indonesia’s two largest Muslim organisations, several school leaders have welcomed the US aid.
“I agree that we have to be careful in accepting any aid from anyone. But I think the US really can’t do much to change the curriculum of our schools. So, I don’t see why we should not accept the aid,” said H Romadhon, the principal of Pesantren Asy-Syifaa, Jakarta.
Meanwhile, the Indonesian government is also welcoming the US aid and has been reassuring its citizens that it will make sure that there would be no intervention in the country’s educational system.
“The concern that the US will intervene in the pesantrens’ curriculum is a bit overboard,” said Dr H Amin, from the ministry of religious affairs. “Even we from the department of religious affairs can’t intervene in the curriculum. How could an outsider possibly do it?”
Development groups and the United Nations estimate that $5.6 billion in additional aid is still needed to ensure that children in poor countries get a basic education
According to education ministry spokesman H Rusmadi, the aid will be allocated to infrastructure improvements, retraining of teachers and the building of new facilities. “We have no plans in using the fund to change any curriculum,” he said.
Rusmadi also reminded Indonesians that the country’s educational system still has a long way to go in fulfilling it’s obligation to adequate education for the masses and in turn will need a lot more funding to improve. “The US is not the first or only country we receive funds from,” he said.
A recent report released by the Global Campaign for Education, an international coalition of development agencies, teachers’ unions and community groups, looked at 22 rich countries and how much aid they provide to boost education in developing countries.
The US scored 12 out of 100 points and was considered the least generous aid giver when its donations are measured as a proportional share of its national income.
Development groups and the United Nations estimate that $5.6 billion in additional aid is still needed to ensure that children in poor countries get a basic education.
“The extra $5.6 billion needed for education is one-fifth the amount Americans spend on pizza each year and half of what Europeans spend on ice cream,” said Oliver Buston, a senior policy advisor for the development group Oxfam.