Defence solicitors also downed their pens at Paisley and Edinburgh Sheriff Courts yesterday.
The escalating row centres around proposals contained in the Scottish Civil Justice Council and Criminal Legal Assistance Bill.
Lawyers are worried about plans for accused people with a disposable income of £68 a week or more to contribute to the cost of their defence in summary cases.
They are also concerned about moves for solicitors to collect the money themselves, instead of the Scottish Legal Aid Board, and say it will alter the relationship between lawyer and client.
The Glasgow Bar Association (GBA) and Edinburgh Bar Association (EBA) confirmed they were boycotting the cities' custody courts, alongside colleagues at Paisley Sheriff Court.
EBA vice-president Mark Harrower said: "Lawyers are disappointed at the Justice Secretary's approach in recent days, which has been to give an indication in public that he is willing to negotiate with the Law Society and reach a sensible conclusion to this problem, whereas in fact he's refusing to budge.
"Kenny MacAskill has seriously misjudged the feeling amongst the profession."
Law Society of Scotland president and Evening Times columnist Austin Lafferty said: "Solicitors working in legal aid have already borne a series of reforms and fee cuts in a bid to save money from the public purse."
A Scottish Government spokesman said: "We want to continue constructive dialogue between all parties including the Law Society of Scotland as strike action is in nobody's interests."