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Governor Charlie Baker is giving an array of top deputies, from members of his Cabinet to dozens of department heads, a 5.5 percent pay raise in the new year, a first for many since Baker took office four years ago.

Baker’s nine Cabinet secretaries will see their salaries rise from $161,500, the same salary several started at when appointed in 2015, to $170,400 a year. Most members of Baker’s direct staff — 66 in total — will also receive the same 5.5 percent increase, according to a Baker spokesman, because they have not gotten the same “merit” pay raises that other executive branch managers have gotten over the past four years.

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Another 39 agency heads will also receive a raise within the executive branch‘s sprawling bureaucracy, which includes dozens of departments and divisions overseeing everything from energy resources to elder affairs to public safety.

But commissioner salaries aren’t uniform, meaning the exact increase each official receives will vary. For example, Christopher Harding, the state’s revenue commissioner, currently makes $158,000, and will get an $8,690 pay bump. Monica Bharel, the commissioner for the Department of Public Health, has a $140,000 salary and will make $7,700 more next year. And Ronald Amidon, the fish and game commissioner, will get $6,985 added to his current $127,000 salary.

Ronald J. Arigo, Baker’s chief human resources officer, said agency heads or commissioners hired after Jan. 2, 2018, will not be eligible for a raise, nor are any acting, interim or so-called 120-day appointees.

The news comes as an array of Beacon Hill officials prepare to take home bigger paychecks.

Legislative leaders will collect three pay increases in January — to their base salary, their leadership stipends, and their office expenses — thanks partly to controversial legislation they passed nearly two years ago tying parts of their paychecks to the state’s wage levels. It means House Speaker Robert A. DeLeo and Senate President Karen E. Spilka will see a near $12,000 raise, pushing their salaries to $169,100.

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All legislators’ base pay will jump from $62,550 to $66,250.

The state’s six constitutional officers are also due raises, and some will collect substantial increases after turning down previous pay hikes.

Baker has said he will take the position’s full $250,000 pay package — a $185,000 salary and $65,000 housing stipend — two years after lawmakers overrode his veto on the pay raise bill. His total compensation will mark a near $100,000 increase from his current $151,000 salary.

Lieutenant Governor Karyn Polito, who makes $122,000 now, also plans to take her statutorily set $165,000 salary.

But both said that they would not take any additional pay generated by the biennial adjustment tied to state wage levels. For Baker, that could have meant another $20,800, and Polito, an additional $13,700 in annual pay.

Attorney General Maura T. Healey and state Treasurer Deborah B. Goldberg have each said they would take a pay increase to $190,000. Both Democrats turned down the last pay hike in 2017 that would have set their salaries at $175,000, meaning both will see their pay rise by more than $50,000 this time. Healey currently makes just over $136,000, Goldberg $133,000.

State Auditor Suzanne M. Bump, who currently makes $165,000, will accept an 8.3 percent increase, pushing her salary to nearly $179,000. “The law determines the auditor’s salary, and she will accept whatever salary the law dictates,” spokesman Mike Wessler said.

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Secretary of State William F. Galvin has not said whether he’d also accept a raise to $179,000 from his current $160,000 salary. Galvin is “still reviewing the numbers,” his spokeswoman, Debra O’Malley, said Friday.

Matt Stout can be reached at matt.stout@globe.com. Follow him on Twitter @mattpstout