Skinner, 56, who was a Labour MEP from 1999 to 2014, was found guilty of three charges after a trial at Southwark Crown Court in London and jailed for four years.
He claimed thousands of pounds for support staff, which actually funded jewellery, restaurants and hotel stays.
However, one top Labour politician branded the four year sentence as "unduly harsh" and one that reflected the "hatred" British judges have for politicians.
Sentencing Skinner, the trial judge said he had abused trust.
Justice Maura McGowan, told him: "You were trusted by the public and you abused that trust.
"You have not only damaged public trust in individual parliamentarians but also in the democratic institution itself.
"This was a breach of trust of the worst kind - this was a sustained pattern of stealing from the taxpayer."
On Friday, a Labour spokesman said: "Peter Skinner has clearly not upheld the high standards we would expect of an elected representative, he is no longer a member of the Labour party."
Reaction to the conviction came from Jonathan Isaby, chief executive of the TaxPayers' Alliance, who said: "Taxpayers will be pleased to see justice done as someone who stole vast amounts of their money is sent to jail.
"Skinner's case highlights the shameful lack of accountability and transparency in the European Parliament's expenses system, which is clearly open to abuse: the fact that he was able to defraud the system over a period of years shows the inadequacy of current safeguards to protect taxpayers' money from corrupt individuals.
"In the same way that the 2009 MPs' expenses scandal prompted change at Westminster, this case ought to be a wake-up call for the authorities in Brussels to make their expenses system more open and accountable to those of us footing the bills.
"Taxpayers will also want to know how much of their money they are going to recover from this disgraced former MEP."
But one senior Labour politician, who did not wish to be named, told this website, "Considering all the MPs and MEPs who bought houses using the expenses systems and put wives and family members on the payroll, a four year sentence - normally reserved for violent criminals and men who have to be taken out of society - seems unduly harsh."
He added, "But if you are MP or MEP and end up in front of British judges who hate politicians and are often Eurosceptic that is what you have to expect. Now the taxpayer will spend far more on Skinner to keep him in prison than the sums he is alleged to have misused."
UKIP's deputy leader Paul Nuttall told this website, "Skinner has done his crime and will now serve his time.
"The UKIP attitude to MEP wrongdoing is once we find out, we kick them out. This is unlike other parties who sometimes like to reward vice."
Shortly before his conviction on 29 April, Skinner said, "Obviously I have some worries about public trust in politicians but that is all I can say."
Before he entered politics he was an economics and business lecturer. Skinner was elected to the European Parliament as Labour MEP for Kent West in 1994 and then in 1999 for the South East of England Region. He stepped down in 2014.