A new law to increase the number of organs available for transplant has been passed by MSPs.
The move to presumed consent was supported by BMA Scotland
But the Human Tissue (Scotland) Bill stopped short of "presumed consent, which would have required people to "opt out" of being an organ donor.
Deputy Health Minister Lewis Macdonald said such a move could have made organ donation more complicated.
Under the new bill, relatives of a registered organ donor will not have the right to veto the person's wishes.
Anyone with a donor card or who has their name on the Organ Donor Register will count automatically as having given their authorisation.
If a person has not given consent, their family will be asked what their
wishes would have been.
Mr Macdonald said the changes - which will come into
effect in September - would mean more transplant operations could take place.
The move to presumed consent, proposed by Liberal Democrat MSP John Farquhar Munro and supported by the British Medical Association (BMA), was backed by several MSPs.
However, Mr Farquhar Munro's amendment was defeated by 87 votes to 18.
Dr Peter Terry, chairman of the BMA in Scotland, described the decision as "disappointing".
He said that 90% of people in Scotland supported organ donation yet only 21% carried organ donor cards.
"Changing to a system of presumed consent, with safeguards, would have reflected the views of individuals; the very principle of this legislation," he said.
"People in Scotland are dying while they wait for organs."
Mr Macdonald said that under a system of presumed consent, a clinician wishing to obtain an organ would have to contact a family member on every occasion, a situation which he said would not arise under the opting-in system.
About a fifth of people in Scotland currently carry organ donor cards
He told MSPs: "A time may come when it will be safe to presume consent, but that time is not now."
The bill also means that hospital post-mortem examinations will only be
carried out with the authorisation of the person while still alive or the
person's nearest relative.
In the case of a child under 12, permission has to be given by the parents.
And anyone who breaches the law by performing post-mortem tests or retaining organs without authorisation will face a substantial fine and the prospect of up to a year in jail.
Mr Macdonald said those measures meant they had fulfilled a pledge made to families affected by the issue in the past.