Opting out generated hostility among both councils and local authority schools. Many chief education officers now believe that local authority schools - and some councillors - will want revenge.
But Mr Clarke said the Government would not allow the quest to raise standards to be diverted by "four or five fireworks caused by misunderstandings".
Councillors at an Association of London Government conference were told to contact the Department for Education and Employment and the Funding Agency for Schools if faced with irreconcilable difficulties. Mr Clarke said: "Try to build the most constructive relationship you can between the GM and the rest of the maintained school population.
"It is not a question of you saying to GM schools 'Ha, you're back now in the LEA fold' or the GM schools saying 'Yahoo, you've had to adapt to our funding system, we were right all along'. Do whatever you can to get the necessary partnership and agreement."
With 30 per cent of London's secondary schools having opted out and given its complex political make-up, attention will inevitably focus on how the changeover is handled in the capital.
It is clear though that there will be problems. Anne Jarvis, the ALG's deputy chair of the education panel, said: "It takes a long time for local feelings about a school to change."
Mr Clarke told the conference that over the years parents in London had lost confidence in many of the capital's schools and that it was vital to raise standards to win them back.