Officials described the findings as a "fire alarm".
But they warned that there are major problems with the way the data is collected.
The statistics are part of a drive to make the NHS more transparent in the wake of the Stafford Hospital scandal.
Neglect and abuse at Stafford Hospital led to hundreds of unnecessary deaths between 2005 and 2008 and prompted a public inquiry.
While officials called the Risk Adjusted Mortality Index (Rami) a "fire alarm", they warned that problems gathering the data made it difficult to interpret the figures.
Data is collected across the UK and a score of 100 is considered normal. When an NHS organisation scores more than 100 it could be an indicator that the number of patients who are dying is higher than should be expected.
A Labour MP who is advising the prime minister on how the NHS handles complaints said she was shocked by the mortality rate at Wales' biggest hospital.
In the most recent batch of data, the University Hospital of Wales (UHW) in Cardiff has the highest score of any Welsh hospital at 128.
David Cameron appointed Ann Clwyd as an advisor after the Cynon Valley MP complained about the standard of care her husband Owen Roberts received before he died at UHW.
Patients and their families had written to her about their experiences at the UHW and other hospitals, she said.
She added: "I hope this will act as a warning signal to the Welsh government to check on the quality of care that is being offered to patients in these hospitals.
"I am determined to find out the reason for the high death rate at UHW, especially as my husband is now one of these statistics."
Dr Graham Shortland, medical director for Cardiff and Vale University Health Board, said: "We have confidence in our staff and the care and treatment they provide and we are reassured by what we are being told by other accepted systems and methods of reviewing quality and safety.
"However, we are in no way complacent about this and work is already underway to further scrutinise this data and any link to the coding problems that we are currently tackling."
A programme of detailed patient case-note reviews will be expanded, he said.
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During the most recent period recorded, five out of six local health boards in Wales had scores higher than 100.
However, officials warned that higher scores may be due to problems gathering data, rather than lapses in the quality of patient care.
The Rami takes into account other factors about patients, including their underlying health, social factors and their lifestyles.
The way the data is collected is known as coding.
Welsh government officials say that coding in Welsh hospitals has not been as good as in the English NHS.
Other annual adjustments to the index make it difficult to compare mortality rates from year to year.
The Welsh government uses Rami scores as one way of measuring performance in the NHS.
However, it says Rami cannot be looked at in isolation and that reviewing case notes after a patient dies is a better way to find out whether improvements to care are needed.
Ministers committed to making more information available as part of their response to the public inquiry into Stafford Hospital.
Grant Robinson, medical director for Aneurin Bevan Local Health Board, said the inconsistencies in coding made it difficult to turn the index into a league table.
But he added: "Anyone who says this is just coding would be missing an important opportunity to improve care."
He said: "It's important to look underneath the numbers and see what's really going on
"We've compared this to a fire alarm. So what you have to do is go see if there is a fire and the best way to do that is to look inside your hospital, get on the ground, see what's happening to patients, and also see what did happen to patients who've died to see if it could have been done better.
"The statistics we have got are acting as fire alarms, so yes there's the sound of an alarm ringing.
"What we need to know is where the fires are and we need to be very alert and get on top of that when it happens quickly."
Health Minister Mark Drakeford, who was appointed in a cabinet reshuffle last week, said: "The Welsh government is committed to transparency on performance and to improving access to NHS information.
"As from today, anyone in Wales can view a measure of hospital mortality data on local health board and Welsh government websites."
The most recent data available is for the period September 2011 to October 2012.
Cardiff and Vale University Health Board, which had a Rami score of 116, said it had a backlog of 40,000 patient episodes which have not yet been coded.
The University Hospital of Wales in Cardiff - Wales' biggest hospital - had the highest Rami score of 128.
The lowest were University Hospital Llandough, on the outskirts of Cardiff, and Nevill Hall Hospital, in Abergavenny, at 86.
Welsh government deputy chief medical officer Chris Jones said: "The need to improve the timeliness and accuracy of data collection is well understood by chief executives and their boards. Health boards have plans in place to meet the standards required."
Conservative health spokesman Darren Millar said the suggestion that mortality rates were higher in bigger hospitals called into question the Welsh government's reconfiguration of hospitals.
"The new health minister must take immediate action to investigate those hospitals with the highest death rates to ensure that swift improvements are made," he said.
He also pointed out that the most recent figures available to the public were six months old.
Welsh Liberal Democrat leader Kirsty Williams said: "I am in no way comparing it to what happened in Mid-Staffordshire, however, given that there are huge problems in data collection and with LHBs and the Welsh Labour government not having a handle on what's going on, I am concerned that we wouldn't be able to readily identify areas of serious weakness in our hospitals if they arose."
Eleven out of 17 district general hospitals in Wales have higher death rates than should be expected, according to statistics published by the Welsh government.