Group like-for-like sales rose 0.3 per cent in the 36 weeks ended 5 September, including the key summer trading period of July and August. But this was mostly down to the group's Legoland division, where like-for-like sales increased 6.7 per cent.
Merlin's restore theme parks arm - which includes Alton Towers - fell 11.4 per cent over the same period.
Merlin Entertainment's share price was down 0.8 per cent in morning trading.
Why it's interesting
Legoland is still being buoyed by last year's summer blockbuster The Lego Movie. The film, featuring more than three million animated bricks, pulled in £34.3m from audiences in the UK last year.
But customers continue to avoid Alton Towers after a horrific accident earlier this year left four people seriously injured.
Two carriages of the Smiler rollercoaster collided at the start of June, leaving 16 people trapped on the ride. A 17-year-old woman and a 20-year-old woman have subsequently both had a leg amputated, while others sustained serious leg injuries.
It led to Alton Towers being temporarily closed, as well as the suspension of UK theme park marketing and temporary ride closures at two of its other UK theme parks. In July, Merlin issued a profits warning relating to the incident.
"[Group] trading in the period has been consistent with guidance provided at the trading update on 27 July and we continue to expect 2015 underlying profit before tax to be broadly in line with last year," the company said.
"Although difficult to assess at this stage, we continue to believe that there may be an ongoing adverse impact on the resort theme parks operating group profitability in 2016."
What Merlin Entertainments said
"The performance of our Legoland parks operating group has remained strong, with very positive guest satisfaction. However, this has been offset by the impact of reduced visitation across the resort theme parks operating group, primarily at Alton Towers Resort, and euro weakness impacting visitation at our London attractions," Merlin said.
"While near term challenges remain, the group is making good overall progress on its growth strategy. We have significant new investments planned across the estate and are well placed to deliver these in 2016 and beyond."
Merlin Entertainments may be performing well strategically, but visitors are still wary about returning to Alton Towers.