John McDonnell said that there would be "no pact, no agreement, no agreement" to support a Labor-led national unity government.
On the eve of the SNP conference in Aberdeen, the Chancellor of the Shadow again intervened in the debate on independence, stressing that the Labor Party would not hold a second referendum in exchange for support from the SNP to a prime minister of Jeremy Corbyn.
McDonnell shocked his Scottish Labor colleagues in August by declaring that a Labor government should allow Holyrood to hold a second referendum on independence if the MSPs vote for one, contradicting party politics.
Now, he insisted that he had given no signal to the SNP about an independence vote in ongoing negotiations to form a non-bargaining alliance in the Commons that would see Corbyn installed as acting Prime Minister.
The SNP supports the plan, but liberal Democrats and rebel Conservatives refuse any support.
McDonnell said that accepting a referendum on independence would also not be a priority for the new Labor government.
He said, "What we are saying is that we do not think there should be another referendum, it is an absolute distraction when there is enough to deal with.
"As a government, our priority will be to end the austerity, invest in the economy and give people a living wage of £ 10 per hour.
"If, after these years of training, the Scottish Parliament gives a mandate, we will not stand in the way, but it is certainly not our priority and we will say that a referendum is not necessary and , of course, a referendum campaign, we would plead for the maintenance of the Union. "
McDonnell added that while relations with Westminster SNP chief Ian Blackford were good, they were based solely on the prevention of a Brexit without agreement.
He said: "Ian and I have close working relationships to avoid a" no deal ", that is the exact limit of our relationships. Beyond that, we will go to the next elections and the government with a majority.
"If we do not get a majority government, there will be no pacts, no agreements, no agreements with the SNP or whoever it is.
"If they want to vote for our radical program, it's their choice, but will they really vote against the £ 10 living wage, to vote against the end of austerity?"
McDonnell insisted that his latest position put him "on the same page" as the leader of the Scottish Labor Party, Richard Leonard, who was left big and dry by the acceptance of the principle of the second referendum by the Chancellor of Ireland. when he spoke in Scotland in August.
McDonnell said: "I was asked a question at the Edinburgh Festival and I answered it honestly. Richard Leonard and I are on the same page.
"We have clearly explained our position, the way we will proceed, the time scales and the nature of the demand that could reach us."
McDonnell also confirmed that Corbyn's assistant, Andrew Fisher, would write the Labor Party's manifesto detailing the party's position on independence.
Fisher is credited with writing the 2017 Labor Manifesto but left the Labor Leader's office on the eve of the party's conference last month citing the "lack of professionalism, competence and human decency" of some of his relatives .
Since then, Corbyn's influential chief of staff, Karie Murphy, has been demoted to a campaign role at the party headquarters as part of a purge attributed to McDonnell.
The Chancellor of the Shadow said that Fisher would probably stay with the Labor Party.
He said, "I think I persuaded him to stay, virtually.
"We have been working together for almost 15 years and we are not just colleagues, we are close friends."
McDonnell, former trainee priest, added, "As you know, I believe in the power of conversion. I think I can convert it. "