Morrison said he sympathised with Trump's criticisms of the WHO, especially its support of re-opening China's "wet markets", where freshly slaughtered animals are sold and where the outbreak first appeared in the city of Wuhan late last year.
"But that said, the WHO also as an organisation does a lot of important work including here in our region in the Pacific and we work closely with them," Morrison said.
"We are not going to throw the baby out with the bathwater here, but they are also not immune from criticism and immune from doing things better."