Travellers were on Tuesday asked to leave Pilgrim Hospital after putting one of its two helipads out of action.
A spokesman for United Lincolnshire Hospitals Trust, which runs the site, said the travellers put the second helipad out of action - used by the larger Sea King - rather than the one used by the Lincolnshire and Nottinghamshire Air Ambulance.
They said the travellers were there for around 20 minutes.
The travellers then moved onto the Geoff Moulder Leisure Centre. But a spokesman for Boston Borough Council, which runs the facility, said they left after being threatened with legal action.
It is also understood some travellers had also occupied the old railway yard, off Spalding Road, but again have now moved on.