Only 3 per cent of respondents from six departments said the Compact was not integrated in their work at all, while 80 per cent said it was either partly or wholly integrated.
The research also found that although there were still cases of individuals who were unfamiliar with the Compact, particularly at lower levels, most departments seemed to adhere to its broad principles, such as independence, three-year funding and reduced reporting requirements.
"We are pleased with the figures about awareness of the Compact, compared with 10 years ago," said Ruth Etkind, policy adviser at the Commission for the Compact. "There is still a lot of work to be done, but we are optimistic. The very fact that people are getting together to discuss it, as was the case for Sector Independence Day on 4 July, is encouraging."
Among the challenges still to be addressed is the idea that third sector organisations should be allowed to campaign: 14 per cent of respondents said they didn't think charities should be able to campaign on issues for which they are receiving government funding, and another 3 per cent didn't think the third sector should be campaigning at all.
A full report of the survey is expected to be published at the end of July.
The commission has also announced that it is to conduct a legal review of the Compact's BME Code to ensure it remains relevant and takes into account recent developments in equality, diversity, race relations and human rights law. Black and minority ethnic third sector representative body Voice4Change England welcomed news.
"We are delighted that the Commission for the Compact is taking action to strengthen it," said the body's chief executive Vandna Gohil. "We support the review and look forward to engaging the BME third sector in getting a fairer deal."