The two bodies are to discuss how Government will adhere more closely to the Compact.
The Department of Health's decision to withhold £17.85m of funding from charities was the most serious breach of the Compact this year.
Since funding was restored in April, the NCVO and civil servants have been involved in discussions aimed at preventing a repeat of the breach.
In June, the NCVO wrote to the DoH demanding urgent action. A civil servant replied the following month, agreeing to a meeting between the two parties.
Last week three senior DoH officials finally met an NCVO delegation.
"We're heartened that the department suggested the meeting," says Saskia Daggett, Compact advocacy manager at the NCVO. "It shows it is genuinely trying to listen and is serious about the Compact."
She was particularly pleased that a representative of the DoH accountancy team was present so that he could pass on information about the Compact to his team, where awareness of the agreement is at a low level.
"Our key message to the DoH was that it should involve charities right at the beginning of any dealings with the voluntary sector," says Daggett.
"The statutory sector needs to have a more open dialogue and be more transparent. For the voluntary sector, it's a case of reading the Compact and using it quickly."
Under the Compact, charities should have learned within 12 weeks whether or not their applications had been successful, but the delay left more than 100 voluntary organisations in financial limbo until the DoH, under threat of legal action, gave assurances in April that funding would continue.
However, Daggett warned that, although the Compact could be invoked to ensure adequate consultation with the sector takes place if similar disputes arise, it was not a guarantee against ministers making cuts.
"There is a funding crisis in the NHS and there are going to be implications for everybody," she says. "We can't force the DoH to spend money on the voluntary sector, but we can say: 'If you are going to make cuts you have to do it properly and consult with us first.'"
If any charity would like to submit its views to NCVO ahead of the meetings, contact Daggett at firstname.lastname@example.org.