Peter Murrell, who is also Nicola Sturgeon’s husband, was accused by opposition politicians of trying to pressure the police around the former first minister.
However the SNP’s chief claimed the messages have been presented in a way which “suggests a meaning that they do not in reality have”.
Mr Murrell has admitted sending the messages, initially leaked to SNP MP Kenny MacAskill, which include a line stating it would be a “good time to start pressurising” the police and that “CPS action would be a good thing”.
Mr Salmond was acquitted of all charges following a trial earlier this year.
Yesterday, leader of the Scottish Conservatives, Douglas Ross, said the messages meant Mr Murrell’s position as head of the SNP was “untenable”.
However, in a submission to the Holyrood committee leading the inquiry into the handling of harassment complaints against Mr Salmond, Mr Murrell denied the messages showed the existence of a conspiracy against the former first minister.
He said the messages sent after Mr Salmond had been charged by police came after the SNP had been contacted by “individuals who had specific, personal questions in relation to that criminal case”.
Mr Murrell said: “My intention was to advise that their questions should be addressed to the police and not the SNP.
"I acknowledge that I did not express myself well, but I suggest that in the context of such a criminal case, directing people to the police was the only responsible thing to advise.”
Mr Murrell also claimed the second message was a "reflection of the shock, hurt and upset” he felt about the charges Mr Salmond faced, but admitted he should have used more careful language.
He said: “In relation to the second message, this has been presented as following on immediately from the first. That is inaccurate. However, my intended meaning was that any and all complaints should be appropriately investigated.
"As most people will appreciate, the immediacy of text messages lend themselves to informal, shorthand forms of expression but, even so, I would wish on reflection to have expressed myself more appropriately.”