"Stockholm has a fundamentally strong position among Swedish holidaymakers this year and has overtaken Gothenburg as the most popular summer city destination," said Elisabeth Lindgren at SJ in a statement.
The royal wedding and several new attractions have boosted Stockholm's appeal, the SJ travel barometer survey shows.
"The capital is hotter than ever this year as it offers the royal wedding, several new attractions such as SkyView, which runs along the outside of the Globe arena, and the newly opened photographic museum which is expected to be a success. Stockholm has also been named European Green Capital 2010," Elisabeth Lindgren said.
In third behind Stockholm and Gothenburg is the city of Visby on the island of Gotland, which is also nominated top in the holiday resort destination category, alongside the west coast. Stockholm's archipelago, and Öland/Österlen make up the list.
The Gothenburg amusement park of Liseberg remained the number one attraction for Swedes, with the Göta canal and Inland railway completing the trio of favourites.
SJ's travel barometer is an annual survey of Swedish holiday travel plans and is based on 4,200 surveys conducted by Sinitor.
A further survey, conducted by travel magazine Vagabond, shows that Swedes have increased their overseas travel by 17.5 percent over the past decade.
The Vagabond travel barometer, published on Tuesday, shows that 6.8 million Swedes travelled overseas (defined as outside the Nordic and Baltic countries) in 2009.
Spain remained the foreign holiday destination of choice, followed by Germany, Thailand and South Africa.
"Although Spain is the Swedes' most popular destination, we have also seen that Swedes have begun to travel to other destinations during the 2000s," said Per J Andersson at Vagabond in a statement.
Despite the 2000s being characterised by terrorism fears, financial crisis and climate change concern, Swedes increasingly travelled far and wide for their holidays.
"Trips to South Africa, for example, have increased by 800 percent. Thailand, Croatia, Turkey and Egypt have also increased significantly, while many Swedes in the 2000s turned their backs on the previously popular Dominican Republic," Per J Andersson said.
July remains the favourite month to take foreign holidays with 744,000 trips from Sweden made during July 2009. October is also popular, followed by June.
The survey also canvassed why Swedes travel. The main reason given was "to get away from it", followed by "sun and sea", to "find peace and tranquillity" and lastly "to meet the relatives".
The Vagabond travel barometer 2010 is based on monthly interviews with 2,000 Swedes and is conducted in partnership with the Travel and Tourist database (Rese och Turistdatabasen - TDB).