The head of Scotland's main human rights organisation, Alan Miller, has endorsed growing calls for prison inmates to be given a vote in next year's independence referendum, potentially for the first time in any UK poll.

Miller, chairman of the Scottish Human Rights commission, which has some influence within the government, has written to all 128 MSPs at Holyrood (there is a vacancy for the 129th seat after the death of Aberdeen Donside member Brian Adam), telling them that allowing inmates to vote on 18 September 2014 would prove that Scotland is championing civil rights, social justice and reforming offenders.

The Scottish independence referendum (franchise) bill which fails to include prisoners in the voting is being debated in Holyrood on Tuesday: already Tavish Scott for the Scottish Liberal Democrats and Patrick Harvie, for the Scottish Greens, have opposed that ban. (Indeed, the Lib Dems are planning to table an amendment to the bill pressing for votes for short term prisoners.)

Miller's letter carefully avoids calling for a blanket voting rights for all prisoners – presumably to avoid contentious rows over votes for multiple murderers, but he states:

The commission proposes that this section of the Bill be revised to adequately reflect the values placed in Scotland on human rights, social justice and the effective rehabilitation of offenders. It is preferable that the Scottish parliament adopts a system where electoral disqualification is based on reasonable and objective justifications such as the type of crime committed or the length of the sentence.

His intervention follows publication on Sunday of a open letter signed amongst others by Tam Baillie, the Scottish children's commissioner; Amnesty International; Mike Ewart, formerly chief executive of the Scottish Prison Service; and Kaliani Lyle, the Scottish member of the UK Equality and Human Rights Commission - signatures collated by the Howard League for Penal Reform Scotland, which urges the Scottish parliament to give "full and serious debate" to prisoner voting.

While allowing inmates to vote would be another UK first for Holyrood, the measure is explicitly ruled out under the Scottish government's Scottish independence referendum (franchise) bill even though UK referendum legislation gives parliaments complete discretion in deciding who can and cannot vote.

Many civil rights campaigners believe the decision to exclude prisoners, in contrast to giving the vote to around 124,000 16 and 17 year olds in the referendum for the first time, is a political decision driven by Alex Salmond's personal distaste for the measure.

In a blog for the Guardian, John Scott QC, the group's chair, said:

It remains unclear why ministers are so keen to exclude absolutely all convicted prisoners from a poll of such exceptional long-term importance or why indeed they are so against any prisoners being given the civic responsibility which voting brings. They have declined to comment on how barring all prisoners from the most high-profile electoral event of our lifetimes may work against successful rehabilitation.

Despite repeated rulings against the UK by the European court of human rights that banning prisoners from voting breaches EU law, successive Labour and Tory governments have been reluctant to change UK law. David Cameron's coalition is due to publish draft legislation soon, but the prime minister has made clear he abhors the reform.

Miller supported the criticisms levelled by the Howard League and others by pointing out that a large majority of other EU member states, including all the countries often cited by the SNP and independence campaigners as model European democracies, allow prisoners to vote.

He said it was "important to note" that amongst the European countries which bar all prisoners from voting are Armenia, Bulgaria, Estonia, Georgia, Hungary, and Russia.

Miller has told MSPs that the Scottish independence referendum (franchise) bill:

provides us with an opportunity to develop a distinctive alternative to the existing UK blanket ban on convicted prisoners voting in elections. This could be a course which brings us closer to the practice in other European democracies such as Denmark, Finland, Ireland, France, Germany, Sweden and Switzerland.

The Scottish government's position is that the ECHR cases are about general elections and do not explicitly refer to referendums. Miller said the court had stated clearly there was a clear, underlying principle that freedom to vote was a basic human right:

In fact, in a UK case decided in 2005 (Hirst No. 2), the Grand Chamber of the European Court said "… the right to vote is not a privilege. In the twenty-first century, the presumption in a democratic state must be in favour of inclusion.'

Yet, privately, even those campaigning for prisoner votes concede it has unlikely to be introduced by the Scottish government.

But the legal pressures are likely to mount: Tony Kelly, the civil rights lawyer who has taken several prisoner rights cases to the UK and European courts, including votes for inmates, is preparing new legal challenges on the referendum. This issue will continue to dog Salmond's government.