Figures from the National Records of Scotland (NRS) show 38 deaths relating to Covid-19 were registered between March 29 and April 4, bringing the total number of fatalities up to Sunday to 9,997.
Since then, six deaths have been recorded in the daily figures from Public Health Scotland.
NRS also warned that with fewer registrations than usual this week due to the public holiday on Friday, the actual fatality figure may be even higher.
Speaking during a coronavirus briefing on Thursday, national clinical director Professor Jason Leitch said one coronavirus patient death and 364 positive tests were recorded in the past 24 hours.
He had earlier sought to reassure Scots that the AstraZeneca Covid vaccine is safe, after UK regulators said there is a possible link between the jab and "extremely rare" blood clots.
He said the vaccination programme is helping to drive down Covid deaths and he urged people to keep going for their jab appointments.
The Medicines and Healthcare products Regulatory Agency (MHRA) has said that while it has not concluded the vaccine causes rare brain clots, the link is getting firmer - though it insisted the benefits of the jab still outweigh the risks overall.
The regulators have recommended that people aged under 30 should be offered Pfizer or Moderna as alternatives to the AstraZeneca vaccine as the balance of risk is more finely balanced for younger age groups who did not tend to suffer serious Covid illness.
Prof Leitch told BBC Radio Scotland's Good Morning Scotland programme: "If you end up in intensive care there is a one in four chance of a serious blood clot which knocks the other risks out of the park, and therefore vaccinating everybody and everybody turning up for their appointments is the crucial message.
"Ten thousand people have unfortunately lost their lives to this disease in this country and nothing like that number have lost anything, either illness or the few deaths there have been, because of blood clots from AstraZeneca, so these three vaccines are safe, they are effective and they are, crucially in Scotland, available.
"So work your way through the ages, and Covid is the critical thing, so get rid of the incidents, drive down the hospitalisations and the mortality which is what's happening, we've now gone below 50 per 100,000 for the first time in months and that's thanks to everybody's work, but it's also thanks to the vaccination programme.
"The crucial message is if you have a vaccination appointment, if you're offered a vaccine, you should absolutely take it - you do not want Covid."
Prof Leitch said he will be going for his jab appointment on Friday, and he added: "I'll be taking whichever vaccine they give me."
Regulators have recommended that people aged 18 to 29 should be offered the Pfizer, Moderna or other vaccines that come on stream as the programme continues to rollout across the UK.
Asked why everyone could not be offered Pfizer or Moderna if they are deemed to be lower risk than the AstraZeneca jab, Prof Leitch said it is an issue of supply.
He said: "We don't have enough of every other vaccine and they have monitored the risk and the benefit and decided that it's much, much more worthwhile to give you the Pfizer or Moderna vaccine if you're under 30."
When asked whether AstraZeneca should be phased out when supplies of the other vaccines become more available, he added: "No there's no suggestion of that because of the scale of the risk being so tiny."
The MHRA said across the UK up to March 31, there were 79 reports of blood clots accompanied by low blood platelet count among people who had had their first dose of the vaccine, out of around 20 million doses given.
Of these 79 patients, 19 people have died, the regulator said, although it has not been established what the cause was in every case.
The figures suggest the risk of rare blood clot is the equivalent to four people out of every million who receive the vaccine.
The MHRA said those who have had their first dose of the AstraZeneca vaccine should still get their second.