The Alert Line is designed to provide independent support for anyone wanting to raise concerns about practices within the health service.
The Scottish government will also introduce a new Whistleblowing Officer to scrutinise the handling of cases.
Health Secretary Shona Robison said she wanted staff to be able to "speak up without fear".
Ms Robison added: "I have always been clear that health boards must ensure that it is safe and acceptable for staff to speak up about any concerns they may have, particularly in relation to patient safety.
"We will continue to work with the NHS across Scotland to ensure an open and transparent reporting culture where all staff have the confidence to speak up."
The National Confidential Alert Line will be extended for one year from 1 August 2016 to 31 July 2017.
The phoneline, 0800 008 6112, will pass any concerns raised by employees on to the employer or the relevant regulatory organisation for investigation.

US President Donald Trump's two adult sons, Donald Jr and Eric, were at the luxury hotel's grand opening.
About 200 protesters gathered outside the building to chant "dump Trump" before the noon ceremony.
The city's mayor and city council boycotted the event because of the president's controversial statements about immigrants.
Steel fences surrounded the downtown property early Tuesday ahead of the ceremony, but that didn't stop the demonstrations.
The words "hate lives here" were scrawled in chalk outside the CA$360m ($274m/Â£220m) luxury hotel, and people stuck anti-Trump sticky notes to the outside of the building.
Another protest was scheduled to take place in downtown Vancouver for 1600 local time (midnight GMT).
In a statement, the Vancouver police force said the safety of both those attending the event and the general public was a priority. They received help from the Royal Canadian Mounted Police (RCMP) Protective Policing unit, which is responsible for the safety of "Internationally Protected Persons," such as the family of foreign officials.
A spokesperson for the RCMP declined to say how much security cost.
The  Canadian tower was designed by famed architect Arthur Erickson and had a soft launch last month. The building has a distinctive 45-degree twist as it rises upward and is the second-tallest building on the city's skyline.
Mr Trump's sons and his daughter Tiffany bypassed protestors by entering through the back, local media reported.
In a press conference in the hotel's grand ballroom, Eric Trump praised developer Joo Kim Tiah's efforts in getting the hotel and condominium project built.
"We love you, we love the relationship and we're going to have a lot of fun for many years to come," said Eric Trump.
He also said Vancouver was "truly one of the most beautiful places in the world" and "so fitting for the Trump brand".
The mayor of Vancouver and members of his party on the City Council said they would not attend the event. Mayor Gregor Robertson had asked the developers in 2015 to remove the Trump name from the project.
"We're a city that's one of the most diverse in the country," Vancouver city councillor Kerry Jang told CBC News. Trump's businesses, he said, are "really not welcome here."
The luxury hotel and tower in the city was jointly developed by Malaysia-based global property firm TA Global Berhad and Vancouver-based property player Holborn Group. The Trump brand signed on to the project in 2013.
Like similar projects worldwide, the Trump Organization provides branding for the Vancouver development and manages the property, but does not retain a stake.
The Trump Organization is an umbrella company for Donald Trump's investments in real estate, brands and other businesses.
In January, the president said he had formally given "complete and total" control of the Trump Organization's businesses to his two sons in a bid to avoid conflicts of interest, though that plan has been criticised for not going far enough in removing any business conflict.
The two sons also attended the opening of the Trump International Golf Club in Dubai in mid-February.
The Vancouver tower's units were sold out last year at record-setting prices for a Canadian condo project.
A confidential whistleblowing line for NHS staff in Scotland has been extended for a year.
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Vancouver's new Trump International Hotel and Tower has opened with pomp and protests.