Southern rail continues to have the most dissatisfied passengers in Britain, closely followed by other south-east commuter services operated by Govia, according to the latest national passenger survey (pdf).

However, the transport watchdog pointed to “fragile green shoots of recovery” as overall satisfaction ratings increased by three percentage points, with Southern and Southeastern recovering from their 2016 nadirs.

One of the biggest gripes was the quality of onboard wifi, a new category, with the majority of passengers saying it was unsatisfactory or poor on their train.

The biannual survey from Transport Focus, which between January and April asked more than 27,000 passengers across Britain to rate their last journey, found that passengers were significantly happier with punctuality and reliability than last spring, giving the best overall scores for more than four years.

The highest satisfaction scores were achieved by Hull Trains and Heathrow Express, both on 97%. Only 72% of Southern passengers were satisfied with their last journey, while the other services in the same franchise, Thameslink and Great Northern, rated 75% and 79% respectively. The next lowest score was from Southeastern, another commuter service operated by Govia, although its 81% score represented a 10-point leap from a year ago.

Only 30% of passengers were satisfied with the wifi on board – a category that has now overtaken the lack of decent toilet facilities on trains in the level of passenger dissatisfaction.

More passengers reported feeling concerned about their personal security, the only category showing a significant fall, down to 75% feeling satisfied with safety on board.

Anthony Smith, chief executive of Transport Focus, said: “Passengers using services in London and the south-east have seen an improvement with an increase in overall satisfaction from 79% last year to 82% this year.

“Having said that, there is some way to go to reach a more acceptable position. These green shoots are fragile and need nurturing. This recovery will be under pressure from upgrade works, industrial relationship problems and rising passenger numbers. So the industry needs to keep a relentless, ongoing focus on performance and reliability.”

The rail industry said it was pleased with the scores. Jacqueline Starr, of the Rail Delivery Group which represents train operators and Network Rail, said: “There is more to do which is why we are investing to improve and better connect communities across the country with major upgrades to the rail network, thousands of new carriages coming on track and 6,400 extra services a week by 2021.”

The shadow transport secretary, Andy McDonald, highlighted that fewer than one in two passengers were satisfied that their ticket represented value for money, and said: “With promised upgrades delayed or cancelled and fares rising way ahead of wages, it’s disappointing but not surprising that passenger satisfaction remains low. It’s becoming more difficult for the government to justify allowing private and foreign state-owned companies to take money out of the system that should be used to improve services or hold fares down.”