Mr MacDonald said it was unrealistic to expect the government to protect councils' position through legislation or even a concordat.
Instead, councils should urgently consider distancing themselves from direct service delivery in favour of adopting a more strategic role, he said.
'At the end of the day, what will protect local government in Scotland is not a piece of paper, but having the full support of their communities in carrying out their jobs.'
Mr MacDonald referred to ideas such as cabinet-style government and elected provosts as a means of making councils more responsive to communities, but said his own interest was in the enabling model.
'If councils can stand back a little from the actual delivery of services, they can free themselves to take a wider strategic policy view,' he said.
Councils should retain overall responsibility for services, he said, but be flexible about how they are delivered. 'We certainly don't want to hear a giant sucking sound when parliament is set up.'
Rather than representing a loss of influence, Mr MacDonald said councils could even by this means recover wide roles in areas such as housing where their influence had been declining.
These views were expected to form the basis of Mr MacDonald's first speech on local government at a seminar at the University of Edinburgh today.
Mr MacDonald also signalled that the Scottish Office intended to play a full role in helping to shape the relationship between councils and the new parliament.
Membership of the Independent Commission, set up to make recommendations to the parliament on local government, is expected to be announced next week.
However, Mr MacDonald told LGC the commissioners would not simply look at the relationship between tiers of government, but would also 'look hard at the nature of local government itself'.
They were likely to be asked to make interim recommendations to ministers.
'I am very concerned that we don't just set up the Independent Commission and let it go off and quietly deliberate until a Scottish parliament is set up,' he said. 'We've really got to shape the debate between now and then.'