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.
A reporter from a newspaper in Sri Lanka has been shot by a group of unidentified men at his home near the capital, Colombo.