Officials said the government had not been remiss in its duty to make the countrys system more efficient.
Presidential Anti-Graft Commission Chairwoman Constancia de Guzman said in a briefing that past administrations, specifically that of former President Joseph Estrada, could have contributed to the negative perception but added much had been done since.
Presidential Management Staff chief Arthur Yap said while the government could not belie the fact that corruption was endemic, efforts being made to address it should have been considered as well.
De Guzman said it was ironic that the report came at a time when the World Bank had extended a grant of $300,000 to address the governments program on strengthening internal audit units as means to fight corruption in the area of procurement.
"Why would the United States of America extend a $21-million grant from the Millennium Challenge Account if it did not see the positive moves being done and the extent of political will that the leadership has given on this area of governance?" De Guzman argued, referring to a US funding granted to help countries combat corruption.
The American Chamber of Commerce, she noted, also came out with a survey saying corruption in the Philippines was abating with an 11-percent decrease from 2004s 88 percent to 2005s 77 percent.
De Guzman said if the administration of Estrada were included in the assessment, then there was basis for the negative rating.
"We are not questioning, we are saying that we need to take a look at what prompted them to say that. As I mentioned earlier, the covered period was for eight years - 1998 to 2005 and all of us are still aware of what happened in 1998, 1999 and 2000," she said, referring to the corruption scandals that rocked the Estrada administration.
"So if those things were captured, then probably there is a reason to say so but for the years 2001 to 2005 and up to this time, the reforms, the intensified campaign against graft and corruption did merit attention from the USAID and World Bank by giving us additional funds," she said.
Yap said the country is facing a "very grave situation when it comes to anti-corruption problem because of the historical context and perspective that we are coming from, but it does not mean that nothing has been done about it."
"It will be more deplorable if we totally just sweep this under the rug and say there is no problem. That is wrong. We accept that there is a problem and that is the reason why President Arroyo is focusing on anti-corruption programs," he said.
De Guzman and Yap said lifestyle checks, cases against officials accused of corruption and other anti-corruption efforts should have been considered.
Drawn from the responses of more than 120,000 citizens, enterprises and experts provided by 25 different organizations worldwide, the World Bank report showed a sharp decline in the ranking of the Philippines in the control of corruption benchmark from 50.5 percent in 1998 to 37.4 percent in 2005.
The countrys percentile rank means that it is better off than 37.4 percent of all other countries covered by the study based on the index for control of corruption, defined as the extent to which public power is exercised for private gain, including petty and grand forms of corruption and the "capture" of the state by elite and private interests.
In a recent visit to Manila, World Bank managing director Juan Jose Daboub said the Philippines, having one of the most "open" societies in the region with its vibrant private sector, lively civil society organizations and vigorous media, had "fertile" ground for good economic policies to flourish.