Mr Morrison had said he would sit down with the school students, but was a no show.
"I'm always happy to listen. I respect everybody's views," he told reporters on Wednesday morning.
"We don't always have to agree on everything, you know, but we do have to respect each other and we do have to take each other's views seriously.
"Whether that's talking about climate, or whether that's talking about energy, or whether that's talking about the other difficult issues we're dealing with in the parliament this week, you've got to respect everybody's views, you can't run their views down because they have them."
But one group of 11 students gathered out the back of Parliament House in the hopes of speaking to Mr Morrison has not yet had any luck.
Fourteen-year-old Tully Bowtell-Young travelled solo from Townsville for the chance to share her concerns with the prime minister - using her own pocket money to help cover costs.
"I think it's worthwhile because nothing I have now is going to mean anything if I don't have a future in this world," she told AAP.
Students protest in Parliament House great hall against Adani mine proposal
The striking students want federal policymakers to stop the Adani coal mine and move Australia from fossil fuels to 100 per cent renewable energy.
They also want the government to respond to their 20,000-strong protests that were held across the country last week, says 16-year-old Aisheeya Huq.
"We have been trying so much for the possibility of meeting with (Scott Morrison) but if we don't get that opportunity after coming so far and going through so much to be here I think we will be a bit disheartened," she told AAP.
The group of students tried numerous times to call the prime minister's office but were told they needed to have a pre-arranged meeting organised - in some instances they were hung up on.
Senator Jordan Steele-John and Independent MP Kerryn Phelps both came out to meet with the students.