Sunday Leader's Faraz Shauketaly, who holds dual British and Sri Lankan citizenship, was rushed to hospital after being shot in the neck.
A doctor who treated Mr Shauketaly said the journalist was now out of danger.
Rights groups say more than a dozen media employees have been killed in Sri Lanka over the past decade.
None of the murders has been solved.
The BBC's Charles Haviland in Colombo says Mr Shauketaly was on the phone to a colleague at the Sunday Leader on Friday evening at his home in Mount Lavinia when the call was cut.
Shortly afterwards he answered a call and said he had been shot in the neck by three intruders, who had then escaped.
A group of foreign lodgers at his house said he was covered in blood and calling for help.
Mr Shauketaly, 52, was taken to intensive care, where doctors pronounced him out of danger and have been working to remove a bullet.
Mr Shauketaly holds British and Sri Lankan passports and the UK government has called on the authorities to bring the attackers to justice.
Our correspondent says Mr Shauketaly had voiced fears that his investigative reporting might be putting him in danger, especially after strangers had called at his house recently asking for his whereabouts.
Four years ago, the Sunday Leader's editor, Lasantha Wickrematunge, was shot dead by a group of masked men on motorbikes.
The case, which has never been solved, highlighted the dismal state of press freedom in the country, analysts said.
"There has been a range of attacks in Sri Lanka on journalists, civil society organisations and others in recent years. To date, too many incidents have had little investigation and no resolution," UK Foreign Office Minister Alastair Burt said in a statement.
The Sunday Leader had long had a reputation for being outspokenly anti-government.
Its profile changed last year when it was bought by a well-connected businessman and retracted some of its articles, but it still does a considerable amount of investigative reporting.
Last month, Sri Lanka was placed 162nd out of 179 in a Press Freedom Index compiled by Reporters Without Borders.

BBC News NI  will provide audiences with its most extensive election coverage to date on our news website.
Users will be able to follow live feeds of what is happening in their own constituencies, with stage by stage results for every seat. Live streams across all 18 battlegrounds will deliver the latest audio, video and news updates from the count centres.
Also on our news website we'll have Northern Ireland-wide results, infographics and analysis from BBC News NI's team of political correspondents; social media updates from every count; and we will stream audio and video feeds of our television and radio output to ensure no election action is missed.
As well as our website coverage, special live programming will start on BBC One NI at 14:30 BST on Friday, 6 May and continue throughout the day as results start to come in.
Coverage will move to BBC Two NI from 19:00 to 22:00 BST, before returning to BBC One NI from 22:35 BST. The election results breakdown coverage will continue on Saturday, 7 May from 10:30 BST.
From 14:00-22:00 BST on Friday, May 6 and 10:00 to 13:00 BST on Saturday, 7 May, BBC Radio Ulster will bring listeners news and analysis on all the latest election results and hear the action from the constituency count centres.
On Friday, 6 May, Radio Foyle will feature an election special from 16:00-22:00 BST, co-presented by Enda McClafferty at the count centre in Londonderry and Elaine McGee in the BBC Radio Foyle studio.
On 8 May, an hour-long special Sunday News at 13:00 BST, will bring listeners all the latest election news.
"BBC News NI reporters will be at every count to bring you the results as they come in and, for the first time, you will be able to follow the stages of every count on BBC News NI Online," Kathleen Carragher, head of BBC News NI, said.
"We'll also have political reaction and analysis from the politicians themselves and from commentators. And the audience can, of course, join the debate through texting and social media."
A reporter from a newspaper in Sri Lanka has been shot by a group of unidentified men at his home near the capital, Colombo.
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With the assembly election now upon us, BBC News NI 's multi-platform coverage will be bringing you all the results as soon as they come in.