Galbraith told Al Jazeera on Saturday: "It is now time to close down those ghost polling centres, these are places where a large number of votes were recorded but they never actually opened.
"And ... in each and every case where there was fraud election commission staff either committed the fraud, co-operated with those who committed the fraud or failed to report it.
"All those staff need to be replaced, not just the 200 who are going to be replaced," he said.
"The head of the UN mission needs to stop pretending the independent election commission is an independent body. All its member were appointed by Karzai and it made partisan decisions at every stage in the process."
Farhan Haq, a spokesperson for the Ban Ki-moon, the UN secretary-general, rejected many of claims that Galbraith made and defended the work of the two electoral bodies in Afghanistan.
"Mr Galbraith neglects to mention is that there are two, not one, electoral bodies in Afghanistan. One of them, the Independent Election Commission, does indeed have members who have been appointed by the government of Afghanistan or have been linked to the current government," he told Al Jazeera.
"The other one however, is the Electoral Complaints Commission, three of whose five members are in fact appointed by Kai Eide [head of the UN mission in Afghanistan] and who are in fact international experts of electoral affairs.
"The electoral complaints council was in fact responsible for throwing out hundreds of thousands of ballots that they believed were tainted one way or another to fraud or irregularity, so to say that the electoral bodies as a whole did not work is incorrect."
Galbraith's warning came as a muted 12-day campaign ahead of the runoff between Karzai and Abdullah Abdullah, a former foreign minister, got under way.
"For us the only constitutional way of establishing a new government is to go to a second round"
Karzai's campaign spokesman
Al Jazeera's Jonah Hull, reporting from Kabul, said that neither camp planned to hold any major rallies over the coming days.
"Questions raised about that suggest that possibly there is some inertia inside these two campaigns - trying to grease the wheels to get going all over again," he said.
"Some [are] suggesting that they're [Karzai and Abdullah] simply having a hard time trying to figure out where they need to concentrate their campaign with so little time to do it.
"And, of course, there is additional speculation that perhaps the two camps are talking to each other, still trying to come up with some sort of a coalition deal that might avoid the need for a second round altogether.
"But that seems unlikely - Dr Abdullah has come out saying there is no way he wants to sit with the Karzai goverment which he left three and a half years ago."
Waheed Omar, Karzai's campaign spokesman, has also dismissed any power-sharing deal.
"For us the only constitutional way of establishing a new government is to go to a second round," he said.Taliban threat
Security fears also remain for the runoff after the Taliban warned voters that its fighters were planning to target voters.
"The Islamic emirate [of Afghanistan] once again informs all the people that no one should participate in this American process and should boycott the process," a Taliban statement emailed to the AFP news agency said.
"The mujahidin are fully prepared to defeat this process. Anyone who participates and gets hurt will be responsible for their own losses."
Sources told Al Jazeera that Mullah Omar, the Taliban leader, had instructed his commanders to block roads leading to polling stations a day before the election and increase attacks on international forces.
A campaign of Taliban violence in the run-up to the first round poll was blamed for keeping voter turnout below 40 per cent.