Environment minister Elliott Morley has pledged action to protect the river Thames from untreated sewage.
Thames Water is waiting for the green light from government
Thousands of fish were killed after 600,000 tonnes of sewage was forced into the river during Tuesday's storms.
Mr Morley said "doing nothing was not an option" to prevent a similar catastrophe happening again.
But a proposed £2bn sewage tunnel under the river to protect London's wildlife might prove too costly and slow to build, he added.
Thames Water is waiting for an indication from the Department for Environment, Food and Rural Affairs as to how it should deal with the problem.
Environmental campaigners say the 22 mile long tunnel under the Thames' riverbed is needed to relieve the capital's overloaded sewage system.
But the scheme - known as Tideway - would add about £12 a year to the average water bill.
Earlier this week, water regulator Ofwat rejected water industry calls for extra cash to fund big infrastructure projects in order to keep bills down.
Mr Morley denied environmental protection was at the bottom of Ofwat's priorities - and said money for environmental protection would have to be made available.
"There will have to be investment in terms of dealing with the storm overflows.
"But you have got to bear in mind that the recent overflow we have had is a one in 60 year event. It wasn't normal.
"But with global warming, of course, and climate change it may well be that such events are more frequent in the future."
Thousands of fish died after sewage flooded into the Thames
He did not rule out giving the green light to Tideway but said cheaper options - such as paying farmers to allow their fields to be flooded and upgrading existing sewage systems - had to be explored first.
"If it can be done faster and cheaper, then we should look at that option.
"In the end, the tunnel might be the only option and, if that is the case then we might have to seriously consider going ahead with that," he told BBC Radio 4's Today programme:
London's 140-year-old sewage system is in urgent need of renewal but at the current rate of repair some pipes will have to last 1,000 years, according to the Institute of Civil Engineers.
Tuesday's problems were caused because the system still pushes water into the Thames through about 60 storm overflows.
The alternative would be allowing it to flood homes and streets.
Following Tuesday's storms, The Environment Agency said dead fish were visible in the river at Kew, Brentford and Isleworth in west London.
A clean-up operation is under way to stop more bream and roach dying.
Thames Water has launched its oxygenating vessels which help improve the quality of the water.