Another half million is invested in the controversial mining giant, BHP Billiton.
Anti-smoking campaigners last night said the Parliament had a "moral duty" to disinvest in tobacco as it undermined public health policy.
The shareholdings appear in the annual accounts for the Scottish Parliamentary Pension Scheme (SPPS), which were published last week.
With a total value of £36.9m at the end of the March 2012, the SPPS is the dedicated pension scheme for all 129 MSPs, as well as the Lord Advocate and Solicitor General for Scotland.
All its investments are in a single pooled fund run by independent manager, Baillie Gifford.
The accounts show two tobacco giants in the "top 10" of the fund's shareholdings last year.
British America Tobacco (BAT) accounted for 1.6% of the fund, and Imperial Tobacco 1.2%, making the SPPS holdings worth just over £1m in total.
BAT and Imperial are the second and fourth-largest tobacco companies in the world, and last year sold 1.1 trillion cigarettes between them.
The use of tobacco companies by the fund comes as stock markets struggle worldwide. Tobacco is traditionally seen as a "safe haven" for investment.
Indeed, some argue pension funds have a financial "duty" to invest in tobacco to maximise returns.
The Scottish Parliament led the way in the UK by banning smoking in public places in 2006, and has since passed laws to crack down on the display of cigarettes and tobacco in shops, and on the use of cigarette vending machines.
The SPPS has four MSPs as trustees – Tory Alex Johnstone, the SNP's Gil Paterson, Labour's David Stewart and its chair, the LibDem Tavish Scott.
The Parliament last night said that because SPPS was only one investor among many in a pooled fund, it could not dictate the shareholdings.
However, Louise Rouse, director of engagement at FairPensions, the campaign for fair investment by pension funds, said MSPs could lobby the trustees to invest in another kind of fund.
"If MSPs were concerned about the investment strategy from an ethical point of view they could raise that with the trustees," she said.
In Australia, the taxpayer-owned Futures Fund, a pension pot for public servants, is currently reviewing whether to end its £140m investment in tobacco firms on ethical grounds.
Sheila Duffy, chief executive of the anti-smoking charity ASH Scotland, said: "Tobacco isn't like any other consumer product, in that when used exactly as intended long-term it will reliably kill one in two of its consumers.
"Any investment in tobacco companies is an investment that undermines public-health policies.
"We know that tobacco companies are looking to increase their market share and we know that spreads an epidemic of disease and early death, which Scotland has suffered badly from.
"I think there's a moral duty to disinvest in tobacco and I would like to see the Scottish Parliament take a lead in this."
Mining firm BHP Billiton has been repeatedly criticised over its labour relations and mining operations in developing countries, and is currently expanding into the controversial "fracking" method, for extracting for shale gas in the US,
A spokesman for the Scottish Parliament said: "The members' pension scheme is part of a pooled fund run by the independent investment manager Baillie Gifford, which operates in accordance with the United Nation's Principles for Responsible Investment.
"The Parliament is only one of a large number of investors in the fund and cannot therefore direct where investments are made."
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