"We have to anticipate any security problems during her visit including any possible terror attack," he told the AFP news agency.
Clinton will be in the world's most populous Muslim-majority country for two days.
Clinton said the Obama administration promised to listen more [EPA]
Hassan Wirajuda, the Indonesian foreign minister, said talks on Wednesday and Thursday are expected to focus on South-East Asia's growing importance in the region, the Iranian nuclear dispute and the war in Afghanistan.
Clinton, who was appointed secretary of state last month, will be holding talks with senior government officials including the Indonesian president before travelling to South Korea and China later in the week.
Earlier this month, the US state department said that the visit to Indonesia was part of efforts to reach out to Muslims around the world.
In his inauguration address on January 20, Barack Obama, the US president, vowed to seek a "new way forward" with Muslim majority countries, "based on mutual interest and respect".
"We should promote ourselves as an example of Islamic democracy"
Christianto Wibisono, US-Indonesia expert
On Monday around 100 members of the Muslim group Hizbut Tahrir rallied against Clinton's visit, saying it was part of a US plan to "divide and rule" Muslims around the world.
Many Indonesians were opposed to the "war on terror" launched by the previous US administration and are now hoping that Obama will bring with him a significant shift in direction.
Analysts say Obama, who spent several years of his youth in Jakarta, could be trying to capitalise on his emotional ties to Indonesia as he seeks to improve relations with the Muslim world.
"Indonesia, in turn, should capitalise on that access," Christianto Wibisono, an expert on US-Indonesian relations, told The Associated Press.
"We should promote ourselves as an example of Islamic democracy."
Indonesia is home to Jemaah Islamiyah, a regional group which has carried out a series of suicide bombings targeting Western interests since 2002.
But experts say a police crackdown has severely weakened the movement, with the last attack occurring more than three years ago.