Lincoln receives September salary warrant for $2,022.33 which is $61 under previous warrant as result of 3 per cent income tax deduction. Pratt, Personal Finances, 182.
Income Tax $61.00
Income tax was first collected under the general revenue act, ap|proved July 1, 1862. A tax was imposed upon the salaries of federal officials at the rate of three per cent on incomes in excess of $600, and the disbursing officers were required to withhold the "income duty," as it was called, at the time of the payment of the salary.
Some time was required to set up the machinery of collection, with the result that the first withdrawal of $61 from Lincoln's salary warrant was not made until September, 1862. Thereafter his warrant was reduced from $2,083.33 to $2,022.33 a month.
source: http://quod.lib.umich.edu/l/lincoln2/5250244.0001.001/1:17.4?rgn=div2;view=fulltext
The deduction was for his $61 "Income duty" (aka Income taxes)
"Income tax was first collected under the general revenue act, approved July 1, 1862. A tax was imposed upon the salaries of federal officials at the rate of three per cent on incomes in excess of $600, and the disbursing officers were required to withhold the "income duty," as it was called, at the time of the payment of the salary. Some time was required to set up the machinery of collection, with the result that the first withdrawal of $61 from Lincoln's salary warrant was not made until September, 1862. Thereafter his warrant was reduced from $2,083.33 to $2,022.33 a month." http://quod.lib.umich.edu/l/lincoln2/5250244.0001.001/1:17.4?rgn=div2;view=fulltext
(Lincoln received the warrant for his September salary on Oct 6, 1862) http://www.thelincolnlog.org/Results.aspx?type=CalendarMonth&year=1862&month=10.
In order to pay for the war, Congress passed legislation signed on July 1 1862 imposing a tax on income. Some time was required to set up the machinery of collection, with the result that the first withdrawal from Lincoln's salary warrant was not made until September, 1862. When Mr. Lincoln received his September paycheck in October, his net salary was $2022.33, $61 (3%) less than his previous paycheck.
Source: Personal Finances of Abraham Lincoln http://quod.lib.umich.edu/l/lincoln2/5250244.0001.001/1:17.4?rgn=div2;view=fulltext