Green startups finding it difficult to find green

"With the dollars that you put in now, you will own a greater percentage of the company," said Nth Power's Tong. "It's really a buying opportunity right now."

Once the downturn is over, many noted, the fundamental reasons for investing in clean energy will not have changed.

"There is an increase in urbanization, a population explosion, and a reliance on fossil fuels which are warming the planet," Schwaber said. "None of these have changed because of the subprime meltdown."

Indeed, The Cleantech Group's Fan said venture firms that committed to the sector before it was hot, such as Kleiner Perkins Caufield & Byers, Khosla Ventures and VantagePoint Venture Partners, were unlikely to pull back now, though they may focus on less capital-intensive businesses.

"It's the second-tier VC firms, the fringe players, the newcomers that are getting scared off," Fan said.