Scientists made the discovery after studying data on 380 families with members who survived into their nineties.
Previously, other research has stated people lacking the vitamin are more at risk from premature death and a host of conditions including heart disease, diabetes, cancer and mental illness.
As a result, the Scottish Government has been under pressure to issue free vitamin D supplements.
In the new investigation, Dutch scientists examined data from the Leiden Longevity Study, which involved families with at least two very elderly siblings – either a brother aged at least 89, or a sister aged 91 and over. A total of 1038 offspring of the elderly siblings were also included, along with partners.
Vitamin D is created in the skin by the action of sunlight, and also obtained from food or supplements, but genetic factors also influence blood levels in different individuals.
The scientists looked at the influence of genetic code alterations known as single nucleotide polymorphisms (SNPs) in three genes associated with vitamin D levels. Their findings are reported today in the Canadian Medical Association Journal.
The authors, led by Dr Diana van Heemst, from Leiden University Medical Centre, wrote: "We found the offspring of nonagenarians who had at least one nonagenarian sibling had lower levels of vitamin D than controls, independent of possible confounding factors and SNPs associated with vitamin D levels."
Offspring of long-lived individuals were also less likely to have a common genetic variant in a gene called CYP2R1, which predisposes people to high levels of vitamin D.
The new results throw doubt on the idea that low levels of the vitamin in the blood can lead to health problems, according to the researchers.
Previous studies have tended not to show whether low vitamin D caused disease or resulted from it, they say.
The scientists wrote: "In the case of mortality, low serum vitamin D levels might be a marker of frailty, because ill patients are expected to spend less time outdoors and may have inadequate nutrition."
The new research suggested that naturally low levels of vitamin D may go hand-in-hand with a genetic resistance to ageing.
In February, vitamin D pressure group Shine on Scotland attacked Holyrood ministers.
It said more action was needed to avoid youngsters contracting conditions such as rickets, or adults developing multiple sclerosis (MS).
Scotland's Chief Medical Officer, Sir Harry Burns, has reiterated guidelines for people to guard against the risks of deficiency, and with other health chiefs sent a joint letter to medical professionals.