Westminster ministers last night put the blame on returning officers for allowing counting machines at May's elections to reject many voting papers without any human oversight.

A BBC Newsnight Scotland investigation discovered that many of the 14,000 ballot papers were rejected as spoiled through a process of "auto-adjudication".

Political parties, whose candidates and agents present at the counts did not realise that many papers did not go through a human adjudication process, were quick to blame the Scotland Office, which was ultimately responsible for the ill-fated arrangements in May. But a spokesman for the Scotland Office responded: "The allegation that the Scotland Office took the sole decision on auto-adjudication is completely untrue and without foundation.

"Decisions on the election were taken as part of a collective decision-making process by the Scottish Executive, Scotland Office, returning officers and other relevant stakeholders."

On the latest specific allegation, he said: "In the instance of auto-adjudication for the count on May 3, the decision was taken between returning officers and the e-counting provider. The Scotland Office did not, at any stage in the process, overrule those decisions or give instructions to the contrary."

Holyrood ballot papers had two columns, one for the constituency vote and one for the regional list. Where papers were wrongly marked, with numbers instead of crosses or with two crosses in one of the columns, these would go for adjudication by the returning officer's staff observed by party representatives.

But it has now emerged that if one of these columns had no marking on it at all, the machines were programmed to reject that as a spoil, while accepting a valid vote in the other column.