The organisation issued a statement after a week of polls which produced markedly different outcomes.
YouGov (59-26%) and TNS-BMRB (47-25%) both suggested a clear No vote majority, while Panelbase's findings, commissioned by the SNP, were 44-43% in favour of independence.
Panelbase's statement read: "There has been some discussion on Twitter of an organised sign-up of Yes campaigners, hoping to influence Panelbase polls.
"In fact new joiners have had no significant effect on our results but we do recognise the potential for abuse of the system if people on either side were able to co-ordinate a mass sign-up of new members.
"As a precaution, between now and the referendum we will not be including results from panel members who joined more recently than June 2013. This only applies to political polls."
The SNP, which has issued three press releases this week based on aspects of the Panelbase poll, said: "We have no knowledge of people signing up."
Earlier this week, Professor John Curtice of Strathclyde University suggested that Panelbase's findings might be different to the others because it did not ask first about independence referendum voting intentions, ahead of all other related questions.
Panelbase said in its statement: "We accept that it is not inconceivable that this may have had some limited effect - although we cannot really know for sure.
"We believe that most of the difference between the results of our usual polls and those of other polling companies lies with the varying approaches we each have to the analysis of the data, rather than in the raw data itself.
"We are using the same methodology that we used before the 2011 election, where we were in line with other contemporary polls.
"We chose to continue with that methodology for the referendum polling but the bottom line is that all pollsters are in pretty uncharted territory - whereas Holyrood and Westminster elections come around regularly and can be used to hone techniques, an independence referendum is a rare event.
"The one thing we polling agencies all have in common is the desire to produce accurate results."