In a previously secret board paper disclosed to the Sunday Herald under freedom of information (FoI), Electoral Commission officials said the lengthy "unregulated period" up to summer 2014 posed serious questions about maintaining public confidence in the system.
They recommended extending the regulated period before the vote, during which tight rules apply, from a standard 16 weeks to about nine months, and the board decided to keep the issue under review.
The Sunday Herald first exposed the "Wild West" nature of the referendum in June.
With the legislation setting out the rules not due to clear Holyrood until late 2013, the campaign until then is literally lawless, with no controls on spending or donations.
Under the Scottish Government's current plan, only in the 16 weeks leading up to the vote would campaigners need to declare and limit their donations and spending. Foreign donations over £500 would then be banned.
In previous referendums, the length of the unregulated period has not been an issue because it has typically been very short. The 1997 referendum on Scottish devolution was held just four months after Labour won power.
The longest unregulated referendum period to date has been about six months, when New Zealand reconsidered its voting system in 2011. But with the Yes Scotland and Better Together campaigns already launched, the period for the independence ballot, expected in October 2014, is four times as long.
Both campaigns say they will refuse foreign cash and self-publish donations, but there is no sanction if they change their minds.
In the paper to the Electoral Commission board in June, officials warned of "the potential for significant levels of uncontrolled campaigning".
They concluded: "The view of Commission staff is that the [regulated] period should be longer than the minimum 16 weeks." In the end, the Commission board chose not to advocate a longer regulated period.
Scottish LibDem leader Willie Rennie said: "The Electoral Commission are right to be concerned and the SNP should act to resolve the problem they have plunged us into. An early referendum would help make this a fair campaign."
A Scottish Government spokesman said: "The referendum will meet the gold standard in terms of fairness, transparency and propriety. Following the AV referendum in 2011 the Electoral Commission recommended that at future referendums the statutory minimum referendum period should be increased from 10 to 16 weeks. "That is exactly what the Scottish Government has proposed in its draft referendum bill."