Pakistan's government has been heavily criticised at home and abroad over perceived corruption, which many attribute to the slow pace of donations to the UN's flood appeal, which has raised two thirds of its 460 million dollar goal.
"I don't want some people to use it (corruption) as an excuse not to give assistance," Jolie told reporters at the UN refugee agency's Islamabad office.
"I have seen what they have done in the field. I've physically seen people assisted, so if you are nervous about giving money directly in one way there are other ways to do it," she said.
The UN refugee agency (UNHCR) said its own appeal is only half-funded, and Elisabeth Byrs, spokeswoman at the Office for the Coordination of Humanitarian Affairs, said extra monies were "still stagnating".
Jolie, clad in a grey dress and black head scarf, spoke after visiting the militant-hit northwest of the country, home to 1.7 million long-term Afghan refugees who have fled fighting in their neighbouring country.