The government recently approved applications for tests to be carried out in areas including parts of Horwich, Blackrod and Astley Bridge.
But council leader Cliff Morris said the authority will remain "absolutely" opposed to the scheme.
He said: "The area covered is some of our most beautiful countryside."
However, he admitted that his stance may not ultimately prevent the government from approving fracking projects in Bolton - after ministers recently declared they could bypass local authorities' opposition.
During a full council meeting, Mr Morris was asked by Liberal Democrat councillor Andrew Martin if it was inevitable that the new Conservative government would fast-track fracking applications.
He replied: "It's a difficult one because it is up to the government.
"But they will know now the feelings of the residents and the councillors at this time.
"There is a head of steam among our residents because this is a scar on the landscape.
"We are saying 'no thank you, we don't want any fracking in Bolton, especially not the areas you have designated."
Fracking is a technique for extracting gas or oil trapped between layers of rock by forcing the layers open using water under high pressure.
Anti-fracking campaigners are concerned about the effects of the process and the waste water generated.
Applications to carry out fracking in parts of Lancashire sparked widespread protests earlier this year, before the proposals were rejected.

The National Galleries of Scotland (NGS) said donations had come from as far afield as Los Angeles and Hong Kong to raise £4m to secure the painting.
Public donations totalled more than £260,000, with the biggest donor the Heritage Lottery Fund, who gave £2.65m.
The work, which was being sold by drinks giant Diageo, will be hung in the Scottish National Gallery in Edinburgh before going on tour.
The fundraising bid was launched in February after Diageo announced their intention to sell it.
The 163.8cm x 169cm painting, which features a Highlands red deer stag with 12 points on its antlers, has been in private or corporate hands since it was painted in 1851.
NGS said it was overwhelmed by the public response to the campaign, with donations made from across the world, including from Anchorage and Queensland.
Private trusts and foundations also gave £634,000, while the Art Fund donated £350,000 and the Scottish government £100,000.
Sir John Leighton, director-general of the National Galleries of Scotland said: "We are thrilled that we have been able to secure this iconic work for the national collection.
"The enormous support from the public has been incredible with donations coming from all over the world and from the length and breadth of Scotland and the rest of the UK.
"Thank you so much to everyone who has donated. Your gift has helped to ensure that this magnificent work will be enjoyed by millions of people for generations to come."
The National Lottery and Scottish government have also given £175,000 to enable the painting to go on tour across Scotland. NGS said plans were being for the tour to a "number of venues across Scotland", starting later this year.
Diageo first said it was selling the painting in November, leading to speculation it could fetch in excess of £10m on the global art market.
The drinks firm later agreed to reduce its selling price from £8m to £4m to help it remain in public view in Scotland.
The Monarch of the Glen, which features a "royal stag", is thought to be set in Glen Affric.
The NGS describe the work as "an important Victorian picture that has taken on various layers of meaning, which include its use in advertising and as a Romantic emblem of the Highlands of Scotland."
The leader of Bolton Council has vowed to oppose any attempt to begin fracking in the region, describing the drilling technique as "a scar on the landscape".
[NEXT_CONCEPT]
Sir Edwin Landseer's iconic Monarch of the Glen has been saved for the nation.