The Scottish Labour leader came under attack from the SNP for proposing a scheme similar to one which her party denied the Nationalists while in government during the early years of devolution.
An aide to Ms Alexander made the case for more money in a submission to an independent review of MSPs' allowances set up by the Scottish Parliament.
Sarah Metcalfe, the director of research for Labour at Holyrood, told the review Ms Alexander receives an allowance of 22,466 compared to the 644,000 David Cameron receives as leader of the opposition at Westminster.
In a letter to the review, chaired by Sir Alan Langlands, Ms Metcalfe said: "The Scottish leader's allowance of 22,466 is insufficient to meet the full costs to an employer of a private secretary - never mind public expectations of a leader's office in terms of interest in the party's approach to parliamentary business and policy stances."
She said Labour was being "forced" to look at party or external funding to meet the demands of the leader's post, and to consider whether to use a parliamentary allowance intended for Ms Alexander's work as a constituency MSP.
Ms Metcalfe argued the leader of the opposition in the Scottish Parliament had 46 MSPs, just one behind the minority governing party. By comparison, the leader of the opposition in Westminster with 192 MPs, approximately a third of the House, has in excess of ten times the resources available to him in terms of leaders' allowances.
Last night, Michael Russell, the environment minister who was the SNP's business manager in the first Scottish Parliament, said Labour was complaining about a system it introduced.
He added: "I sympathise with Wendy Alexander in her suggestions for more support, but she would do well to remember why she is in the position she is.
"She should have thought of that before she asked for more money. This is nothing but hypocrisy."
The rules under which payments to the parties are made are designed to prevent staff engaging in party political work outside Holyrood.
They state staff must be restricted to supporting the party leader as a party spokesperson or representative, but staff should not be allowed to campaign or canvas for the party.
No stationery provided to the leader can be used for campaigning, electoral activities or the display of party materials.
The party leader is responsible to the Scottish Parliament Corporate Body, which oversees finances, for observance of this code and is also responsible for the activities of his or her staff.