Bill Gates told CNBC on Tuesday that innovation is key to making clean energy more attractive to countries on a cost basis.

Gates announced on Monday the start of Breakthrough Energy Ventures, a $1 billion clean energy fund, which he plans to chair. Other backers include Alibaba's Jack Ma and Amazon's Jeff Bezos. The fund aims to invest in next generation energy technologies.

In a "Squawk Box" interview, Gates said the idea of the fund started a year ago when he was attending the global climate talks. He wants to make clean energy cheaper than "dirty" energy.

"We want to be cheaper than coal or gasoline for transport. And so that bar is particularly low right now," the billionaire Microsoft co-founder and philanthropist said. "But there are a lot of paths that make us feel confident we can get there. We have five or six paths. We have several companies in each path."

Gates, who recently pitched energy innovation to Trump in a phone call, said he's confident the president-elect would consider his ideas.

"This administration likes a good deal," Gates said, adding he's prepared to lobby Trump on making sure America is on the forefront of energy research and development. "It's not a huge part of the budget and yet it can help the economy just like shale gas has."