It comes hard on the heels of the departure of presidential spokesman, Pedro Luis Rodrigues, and raises the fear of a stampede to leave the administration before the President faces impeachment for his alleged involvement in corruption.
Mr Goldemberg, a distinguished scientist and former rector of Sao Paulo University, with no party political affiliation, is believed to have felt uneasy for some time about the revelations of financial impropriety in the presidential circle that have been appearing in the Brazilian press almost daily since the President's brother, Pedro, set the ball rolling in a magazine interview in May.
For a while Mr Goldemberg had become the key figure in the cabinet, standing in for the controversial environment secretary, Jose Lutzenberger, when he resigned a few months before June's Earth Summit in Rio de Janeiro, and staying on when the President restructured his cabinet at the beginning of April.
Other senior members of the administration, such as the president of the Central Bank, Francisco Gros, are believed to be unhappy about the President's apparent determination to buy political survival even at the expense of an economic austerity programme agreed with the International Monetary Fund in January.
This commits Brazil to strict controls on public spending, but over the weekend the President secured extra resources for the Transport and Social Action ministries to allocate to such schemes as road construction, designed to secure the support of congressional deputies when it comes to voting on the impeachment charges.
Mr Collor needs the backing of 168 deputies, or one-third of the Congress, if he is to survive.
The key figure, as far as the stability of the economic programme is concerned, is the Economy Minister, Marcilio Marques Moreira, a highly respected figure in international financial circles, who was instrumental in securing last month's agreement in principle on the restructuring of dollars 42bn (pounds 22bn) of Brazil's commercial debt. If he were to go now - and observers believe this is unlikely for the present - the good work done in restoring Brazil to financial respectability could rapidly unravel.Reuse content