Stuart Etherington, chief executive of the NCVO, has written to every MP asking them to raise the issue with colleagues at the Department for Culture, Media and Sport, the Treasury and the Office of the Third Sector.
Don Foster, culture spokesman for the Liberal Democrats, will table an early day motion in the House of Commons this week.
Navca, the NCVO and its sister organisations in Wales, Scotland and Northern Ireland are also urging members to get in touch with their local MPs to encourage them to oppose a further raid.
The moves come a month after Liberal Democrat peer Dame Julia Neuberger used her weekly Third Sector column to accuse the sector of not doing enough to prevent BLF cash being used.
Pete Moorey, parliamentary and media manager at the NCVO, said Big Lottery Fund chair Sir Clive Booth's warning a fortnight ago that the sector would lose a further £315m if the lottery was used to cover the reported extra £900m cost of the games (Third Sector, 10 January 2006) had alerted the sector to the severity of the problem.
"That really illustrated the point in quite stark terms," he said. The NCVO approached Treasury officials about the problem in December, according to Moorey, but it "didn't seem to be at the forefront of their minds".
The Big Lottery Fund has calculated that using its cash to meet the extra costs could lead to a reduction in funding for good causes of £500,000 per parliamentary constituency. The lottery has already contributed a total of £1.5bn to the games.
Etherington raised the issue last week with Hilary Armstrong, a minister in the Cabinet Office, whose junior colleague Ed Miliband serves on the Cabinet committee for the Olympics.
A spokesman for the Cabinet Office said: "The Government recognises that the Big Lottery Fund is a crucial source of income for many organisations in the sector, and the Office of the Third Sector will be working closely with colleagues in the Treasury and the Department for Culture, Media and Sport over coming weeks to find an equitable solution to this issue.
"We must both ensure a successful Olympic Games that will create valuable opportunities for the third sector, and also that third sector organisations continue to have access to as large a range of funding as possible."