The "white van" allegations were serious enough to be mentioned by the UNHCR Navi Pillay back in 2013
I asked the Government for more information about the new Commission of Inquiry on Disappearances, and stressed the need for it to be more effective than the five previous commissions of this kind. I was disappointed to learn that it will only cover disappearances in the Northern and Eastern Provinces, which means that the many “white van” disappearances reported in Colombo and other parts of the country in recent years will not fall within its scope.
Gotabaya Rajapaksa is not mentioned by name there. I don't know if there has been a more serious investigation after that.
(As an aside, the Sri Lankan government was quick to accuse Pillay of bias because of her "Tamil descent".)
Note that "white vans" may be more or less figuratively used, to describe other politically related "enforced disappearances". See the documentary White Van Stories for example. The documentary says
After Iraq, Sri Lanka has the highest number of disappearances in the world.
Some mass graves were discovered, including one last year, but the investigations haven't even been able to tell who was buried in many of them. The largest one found (last year) was apparently unrelated, with victims dated to the early Portuguese occupation. (As an aside, in Argentina's "Dirty War" many of the disappeared were thrown into the ocean, according to the testimonies of those participating; the bodies are still not found.)
There in one first-hand accounts of a journalist who said he was abducted in white vans (but survived), namely Poddala Jayantha. He was severely tortured, but his assailants never identified themselves. He blames the government though:
Jayantha doesn’t know who snatched him. But he said he had angered Gotabhaya Rajapaksa, one of the most powerful officials in his brother’s administration with the title of secretary to the minister of defense, by arguing against Rajapaksa’s criticism of the media. Jayantha said he was openly warned of dire consequences of challenging such a formidable figure.
According to a March report by the International Truth and Justice Project — an evidence-gathering organization administered by a South Africa-based nonprofit foundation — the abuse continued beyond the civil war through 2016, well after the country elected a new president who promised accountability for past injustices.
The report is based on testimony from 46 Sri Lankan Tamils who fled to Britain or Switzerland and were once held at Sri Lanka’s security forces’ headquarters. Some victims said they were abducted in a “white van” and held for months or even years without due process; kept in cells so small they could not lie down; beaten, raped or tortured by means of having barbed wire inserted into their anal cavities. The military’s chief aim, they said, was to learn of any ongoing rebel activity as well as the location of hidden weapons caches, according to the report.
Police investigations have not led to any convictions more than two years after hard-line President Mahinda Rajapaksa was defeated by a moderate, Maithripala Sirisena. Only a few high profile cases are being heard in courts at a slow pace while investigations haven’t even begun in dozens of others, mainly those relating to Tamil journalists who were killed or persecuted in the country’s north and east.