The firm, which planned to build a 60-bed hotel, more than 100 holiday lodges and a water park on the site, made the announcement on Tuesday.
It comes after a report from officers at Loch Lomond and the Trossachs National Park recommended the plans were rejected.
The proposals, a joint project between the Yorkshire-based company and Scottish Enterprise, received significant opposition from politicians and members of the public.
More than 57,000 people objected to the plans using a website set up by the Scottish Greens.
West Dunbartonshire Council also rejected the plans in June after being consulted as the neighbouring authority.
Despite the decision to withdraw the application, bosses have not ruled out coming back with an amended bid in the future.
Andy Miller, director of Lomond Banks, said: "We've been working hard with all parties, including the National Park Authority, for more than two years to ensure all information relating to the proposed development was made readily available.
"We know the national park recognises that the majority of what we propose fits in with the local development plan (LDP).
"It is therefore surprising and disappointing that their recommendation report raises previously unidentified concerns and highlights the need for new additional information."
He added: "Our priority now is to fully understand concerns, gather the necessary information and dispel some of the myths that continue to circulate around our ambitions for the site.
"It is only at this point, we will consider re-submitting our plans to ensure decision makers will be able to take a fully informed decision on this important application."
Allan McQuade, director of Scottish Enterprise, said: "Any proposed plan and investment of this scale must be considered from all angles and subsequent planning and investment decisions based on hard evidence and fact therefore it is only right that the current planning application be withdrawn to allow sufficient time for all parties to consider additional new information.
"As with previous developments at Loch Lomond, we understand people are concerned and our priority is to ensure that any development on the parcel of derelict land in Balloch is delivered in line with planning policy."
In a letter to the planning authority, representatives for the applicant said requests had been made to postpone the decision hearing, scheduled to take place on September 24.
Scottish Greens MSP Ross Greer, who spearheaded the campaign against the development, said: "Flamingo Land's environmentally destructive proposal was the most unpopular planning application in Scottish history.
"This is likely a transparent attempt to resubmit with a few small changes, cancelling the near 60,000 objections lodged to the current proposals. If they think such a cynical ploy will stop our community campaign, they have another thing coming.
"We will not stop until we have saved Loch Lomond from Flamingo Land's greed."