The firebrand leader remains popular in the Philippines, but his administration is facing growing criticism over its handling of one of the worst coronavirus outbreaks in Asia.
"At the height of the pandemic, when it began, we had nothing," Duterte said in a weekly late-night national address. "It was costly because of lack of supply."
Opposition lawmakers questioned the government's emergency deals to buy medical supplies from a lowly-capitalised company with links to government officials.
In budget hearings, health ministry officials were grilled on unspent pandemic funds. State auditors have flagged "deficiencies" in more than $1 billion (S$1.3 billion) in Covid-19 funds.
"Senate, do not investigate programmes which are ongoing. You will derail it by your incessant penchant for investigating government offices," Duterte said.
ALSO READ: Philippine health agency hit with coronavirus fraud, whistle-blowers claim
With 2 million confirmed infections and 33,680 deaths, the Philippines has the second highest number of Covid-19 cases and fatalities in Southeast Asia, after Indonesia.
Surging cases driven by the Delta variant are overwhelming hospitals, while healthcare workers have protested to end to what they called government neglect and unpaid benefits.
Duterte, who is banned by the constitution from seeking re-election, plans to run as vice president next year. Critics see it as an effort to extend his power.